Methods of detecting prostate cancer

ABSTRACT

The invention described herein provides biological markers for the diagnosis, prognosis, and monitoring of prostate cancer

RELATED APPLICATION

This application claims priority and benefit from U.S. ProvisionalPatent Application 62/049,281, filed Sep. 11, 2014, the contents anddisclosures of which are incorporated by reference in their entirety.

FIELD OF THE INVENTION

This invention relates generally to using biological markers for thediagnosis, prognosis, and monitoring of prostate cancer.

BACKGROUND OF THE INVENTION

Early diagnosis of prostate cancer often increases the likelihood ofsuccessful treatment or cure of such disease. Current diagnosticmethods, however, depend largely on population-derived average valuesobtained from healthy individuals. Personalized diagnostic methods areneeded that enable the diagnosis, especially the early diagnosis, of thepresence of prostate cancer in individuals who are not known to have thecancer or who have recurrent prostate cancer.

Leukocytes begin as pluripotent hematopoietic stem cells in the bonemarrow and develop along either the myeloid lineage (monocytes,macrophages, neutrophils, eosinophils, and basophils) or the lymphoidlineage (T and B lymphocytes and natural killer cells). The majorfunction of the myeloid lineage cells (e.g., neutrophils andmacrophages) is the phagocytosis of infectious organisms, live unwanteddamaged cells, senescent and dead cells (apoptotic and necrotic), aswell as the clearing of cellular debris. Phagocytes from healthy animalsdo not replicate and are diploid, i.e., have a DNA content of 2n. Onaverage, each cell contains <10 ng DNA, <20 ng RNA, and <300 ng ofprotein. Non-phagocytic cells are also diploid and are not involved inthe internalization of dead cells or infectious organisms and have a DNAindex of one.

The lifetime of various white blood cell subpopulations varies from afew days (e.g., neutrophils) to several months (e.g., macrophages). Likeother cell types, leukocytes age and eventually die. During their agingprocess, human blood- and tissue-derived phagocytes (e.g., neutrophils)exhibit all the classic markers of programmed cell death (i.e.,apoptosis), including caspase activation, pyknotic nuclei, and chromatinfragmentation. These cells also display a number of “eat-me” flags(e.g., phosphatidylserine, sugars) on the extracellular surfaces oftheir plasma membranes. Consequently, dying and dead cells andsubcellular fragments thereof are cleared from tissues and blood byother phagocytic cells.

The prostate specific antigen is currently one of the most widely useddiagnostic measures used to detect prostate cancer. However, falsenegatives and false negatives are common, resulting in mistreatment ofpatients with no prostate cancer or overtreatment of patients withnon-lethal prostate cancer. Thus, improved methods for detectingprostate cancer are needed.

SUMMARY OF THE INVENTION

In one aspect, the present invention provides methods for detecting ordiagnosing prostate cancer by using at least one or more markersselected from Signature 1 (Table 1) and/or Signature 2 (Table 2) and/orSignature 3 (Table 3) and/or Signature 4 (Table 4). Levels (e.g., geneexpression levels, protein expression levels, or activity levels) of theselected markers may be measured from a blood sample, or a portion of ablood sample (e.g., macrophages and non-phagocytes), from a subject.Such levels then can be compared, e.g., the levels of the selectedmarkers in the phagocytic cells and in the non-phagocytic cells toidentify one or more differences between the measured levels, indicatingwhether the subject has prostate cancer. The identified difference(s)can also be used for assessing the risk of developing prostate cancer,prognosing prostate cancer, monitoring prostate cancer progression orregression, assessing the efficacy of a treatment for prostate cancer,or identifying a compound capable of ameliorating or treating prostatecancer.

In yet another aspect, the levels of the selected markers in thephagocytic cells may be compared to the levels of the selected markersin a control (e.g., a normal or healthy control subject, or a normal orhealthy cell from the subject) to identify one or more differencesbetween the measured levels, indicating whether the subject has prostatecancer, the prognosis of the cancer and the monitoring of the cancer.The identified difference(s) can also be used for assessing the risk ofdeveloping prostate cancer, prognosing prostate cancer, monitoringprostate cancer progression or regression, assessing the efficacy of atreatment for prostate cancer, or identifying a compound capable ofameliorating or treating prostate cancer. Some embodiments of theinvention are:

1. A method for diagnosing or aiding in the diagnosis of prostate cancerin a subject, the method comprising the steps of:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 1 markers in a population of the subject'smacrophage cells;

b) measuring the levels of the one or more selected Signature 1 markersin a population of the subject's non-phagocytic cells; and

c) identifying a difference between the measured levels of the one ormore selected Signature 1 markers in steps a) and b),

wherein the identified difference indicates that the subject has saidprostate cancer.

2. A method for assessing the risk of developing prostate cancer in asubject, the method comprising the steps of:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 1 markers in a population of the subject'smacrophage cells;

b) measuring the levels of the one or more selected Signature 1 markersin a population of the subject's non-phagocytic cells; and

c) identifying a difference between the measured levels of the one ormore selected Signature 1 markers in steps a) and b),

wherein the identified difference indicates that the subject has a riskof developing said prostate cancer.

3. A method for prognosing or aiding in the prognosis of prostate cancerin a subject, the method comprising the steps of:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 1 markers in a population of the subject'smacrophage cells;

b) measuring the levels of the one or more selected Signature 1 markersin a population of the subject's non-phagocytic cells; and

c) identifying a difference between the measured levels of the one ormore selected Signature 1 markers in steps a) and b),

wherein the identified difference is indicative of the prognosis of saidprostate cancer in the subject.

4. A method for assessing the efficacy of a treatment for prostatecancer in a subject comprising:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 1 markers in a population of the subject'smacrophage cells before the treatment;

b) measuring the levels of the one or more selected Signature 1 markersin a population of the subject's non-phagocytic cells before thetreatment;

c) identifying a first difference between the measured levels of the oneor more selected Signature 1 markers in steps a) and b);

d) measuring the levels of the one or more selected Signature 1 markersin a population of the subject's macrophage cells after the treatment;

e) measuring the levels of the one or more selected Signature 1 markersin a population of the subject's non-phagocytic cells after thetreatment;

f) identifying a second difference between the measured levels of theone or more selected Signature 1 markers in steps d) and e); and

g) identifying a difference between the first difference and the seconddifference,

wherein the difference identified in g) is indicative of the efficacy ofthe treatment for said prostate cancer in the subject.

5. A method for monitoring the progression or regression of prostatecancer in a subject comprising:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 1 markers in a population of the subject'smacrophage cells at a first time point;

b) measuring the levels of the one or more selected Signature 1 markersin a population of the subject's non-phagocytic cells at the first timepoint;

c) identifying a first difference between the measured levels of the oneor more selected Signature 1 markers in steps a) and b);

d) measuring the levels of the one or more selected Signature 1 markersin a population of the subject's macrophage cells at a second timepoint;

e) measuring the levels of the one or more selected Signature 1 markersin a population of the subject's non-phagocytic cells at the second timepoint;

f) identifying a second difference between the measured levels of theone or more selected Signature 1 markers in steps d) and e); and

g) identifying a difference between the first difference and the seconddifference,

wherein the difference identified in g) is indicative of the progressionor regression of said prostate cancer in the subject.

6. A method for identifying a compound capable of ameliorating ortreating prostate cancer in a subject comprising:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 1 markers in a population of the subject'smacrophage cells before administering the compound to the subject;

b) measuring the levels of the one or more selected Signature 1 markersin a population of the subject's non-phagocytic cells beforeadministering the compound to the subject;

c) identifying a first difference between the measured levels of the oneor more selected Signature 1 markers in steps a) and b);

d) measuring the levels of the one or more selected Signature 1 markersin a population of the subject's macrophage cells after theadministration of the compound;

e) measuring the levels of the one or more selected Signature 1 markersin a population of the subject's non-phagocytic cells after theadministration of the compound;

f) identifying a second difference between the measured levels of theone or more selected Signature 1 markers in steps d) and e); and

g) identifying a difference between the first difference and the seconddifference,

wherein the difference identified in g) indicates that the compound iscapable of ameliorating or treating said prostate cancer in the subject.

7. A method for diagnosing or aiding in the diagnosis of prostate cancerin a subject, the method comprising the steps of:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 2 markers in a population of the subject'smacrophage cells;

b) measuring the levels of the one or more selected Signature 2 markersin a population of the subject's non-phagocytic cells; and

c) identifying a difference between the measured levels of the one ormore selected Signature 2 markers in steps a) and b),

wherein the identified difference indicates that the subject has saidprostate cancer.

8. A method for assessing the risk of developing prostate cancer in asubject, the method comprising the steps of:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 2 markers in a population of the subject'smacrophage cells;

b) measuring the levels of the one or more selected Signature 2 markersin a population of the subject's non-phagocytic cells; and

c) identifying a difference between the measured levels of the one ormore selected Signature 2 markers in steps a) and b),

wherein the identified difference indicates that the subject has a riskof developing said prostate cancer.

9. A method for prognosing or aiding in the prognosis of prostate cancerin a subject, the method comprising the steps of:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 2 markers in a population of the subject'smacrophage cells;

b) measuring the levels of the one or more selected Signature 2 markersin a population of the subject's non-phagocytic cells; and

c) identifying a difference between the measured levels of the one ormore selected Signature 2 markers in steps a) and b),

wherein the identified difference is indicative of the prognosis of saidprostate cancer in the subject.

10. A method for assessing the efficacy of a treatment for prostatecancer in a subject comprising:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 2 markers in a population of the subject'smacrophage cells before the treatment;

b) measuring the levels of the one or more selected Signature 2 markersin a population of the subject's non-phagocytic cells before thetreatment;

c) identifying a first difference between the measured levels of the oneor more selected Signature 2 markers in steps a) and b);

d) measuring the levels of the one or more selected Signature 2 markersin a population of the subject's macrophage cells after the treatment;

e) measuring the levels of the one or more selected Signature 2 markersin a population of the subject's non-phagocytic cells after thetreatment;

f) identifying a second difference between the measured levels of theone or more selected Signature 2 markers in steps d) and e); and

g) identifying a difference between the first difference and the seconddifference,

wherein the difference identified in g) is indicative of the efficacy ofthe treatment for said prostate cancer in the subject.

11. A method for monitoring the progression or regression of prostatecancer in a subject comprising:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 2 markers in a population of the subject'smacrophage cells at a first time point;

b) measuring the levels of the one or more selected Signature 2 markersin a population of the subject's non-phagocytic cells at the first timepoint;

c) identifying a first difference between the measured levels of the oneor more selected Signature 2 markers in steps a) and b);

d) measuring the levels of the one or more selected Signature 2 markersin a population of the subject's macrophage cells at a second timepoint;

e) measuring the levels of the one or more selected Signature 2 markersin a population of the subject's non-phagocytic cells at the second timepoint;

f) identifying a second difference between the measured levels of theone or more selected Signature 2 markers in steps d) and e); and

g) identifying a difference between the first difference and the seconddifference,

wherein the difference identified in g) is indicative of the progressionor regression of said prostate cancer in the subject.

12. A method for identifying a compound capable of ameliorating ortreating prostate cancer in a subject comprising:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 2 markers in a population of the subject'smacrophage cells before administering the compound to the subject;

b) measuring the levels of the one or more selected Signature 2 markersin a population of the subject's non-phagocytic cells beforeadministering the compound to the subject;

c) identifying a first difference between the measured levels of the oneor more selected Signature 2 markers in steps a) and b);

d) measuring the levels of the one or more selected Signature 2 markersin a population of the subject's macrophage cells after theadministration of the compound;

e) measuring the levels of the one or more selected Signature 2 markersin a population of the subject's non-phagocytic cells after theadministration of the compound;

f) identifying a second difference between the measured levels of theone or more selected Signature 2 markers in steps d) and e); and

g) identifying a difference between the first difference and the seconddifference,

wherein the difference identified in g) indicates that the compound iscapable of ameliorating or treating said prostate cancer in the subject.

13. A method for diagnosing or aiding in the diagnosis of prostatecancer in a subject, the method comprising the steps of:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 3 markers in a population of the subject'smacrophage cells;

b) measuring the levels of the one or more selected Signature 3 markersin a population of the subject's non-phagocytic cells; and

c) identifying a difference between the measured levels of the one ormore selected Signature 3 markers in steps a) and b),

wherein the identified difference indicates that the subject has saidprostate cancer.

14. A method for assessing the risk of developing prostate cancer in asubject, the method comprising the steps of:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 3 markers in a population of the subject'smacrophage cells;

b) measuring the levels of the one or more selected Signature 3 markersin a population of the subject's non-phagocytic cells; and

c) identifying a difference between the measured levels of the one ormore selected Signature 3 markers in steps a) and b),

wherein the identified difference indicates that the subject has a riskof developing said prostate cancer.

15. A method for prognosing or aiding in the prognosis of prostatecancer in a subject, the method comprising the steps of:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 3 markers in a population of the subject'smacrophage cells;

b) measuring the levels of the one or more selected Signature 3 markersin a population of the subject's non-phagocytic cells; and

c) identifying a difference between the measured levels of the one ormore selected Signature 3 markers in steps a) and b),

wherein the identified difference is indicative of the prognosis of saidprostate cancer in the subject.

16. A method for assessing the efficacy of a treatment for prostatecancer in a subject comprising:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 3 markers in a population of the subject'smacrophage cells before the treatment;

b) measuring the levels of the one or more selected Signature 3 markersin a population of the subject's non-phagocytic cells before thetreatment;

c) identifying a first difference between the measured levels of the oneor more selected Signature 3 markers in steps a) and b);

d) measuring the levels of the one or more selected Signature 3 markersin a population of the subject's macrophage cells after the treatment;

e) measuring the levels of the one or more selected Signature 3 markersin a population of the subject's non-phagocytic cells after thetreatment;

f) identifying a second difference between the measured levels of theone or more selected Signature 3 markers in steps d) and e); and

g) identifying a difference between the first difference and the seconddifference,

wherein the difference identified in g) is indicative of the efficacy ofthe treatment for said prostate cancer in the subject.

17. A method for monitoring the progression or regression of prostatecancer in a subject comprising:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 3 markers in a population of the subject'smacrophage cells at a first time point;

b) measuring the levels of the one or more selected Signature 3 markersin a population of the subject's non-phagocytic cells at the first timepoint;

c) identifying a first difference between the measured levels of the oneor more selected Signature 3 markers in steps a) and b);

d) measuring the levels of the one or more selected Signature 3 markersin a population of the subject's macrophage cells at a second timepoint;

e) measuring the levels of the one or more selected Signature 3 markersin a population of the subject's non-phagocytic cells at the second timepoint;

f) identifying a second difference between the measured levels of theone or more selected Signature 3 markers in steps d) and e); and

g) identifying a difference between the first difference and the seconddifference,

wherein the difference identified in g) is indicative of the progressionor regression of said prostate cancer in the subject.

18. A method for identifying a compound capable of ameliorating ortreating prostate cancer in a subject comprising:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 3 markers in a population of the subject'smacrophage cells before administering the compound to the subject;

b) measuring the levels of the one or more selected Signature 3 markersin a population of the subject's non-phagocytic cells beforeadministering the compound to the subject;

c) identifying a first difference between the measured levels of the oneor more selected Signature 3 markers in steps a) and b);

d) measuring the levels of the one or more selected Signature 3 markersin a population of the subject's macrophage cells after theadministration of the compound;

e) measuring the levels of the one or more selected Signature 3 markersin a population of the subject's non-phagocytic cells after theadministration of the compound;

f) identifying a second difference between the measured levels of theone or more selected Signature 3 markers in steps d) and e); and

g) identifying a difference between the first difference and the seconddifference,

wherein the difference identified in g) indicates that the compound iscapable of ameliorating or treating said prostate cancer in the subject.

19. A method for diagnosing or aiding in the diagnosis of prostatecancer in a subject, the method comprising the steps of:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 4 markers in a population of the subject'smacrophage cells;

b) measuring the levels of the one or more selected Signature 4 markersin a population of the subject's non-phagocytic cells; and

c) identifying a difference between the measured levels of the one ormore selected Signature 4 markers in steps a) and b),

wherein the identified difference indicates that the subject has saidprostate cancer.

20. A method for assessing the risk of developing prostate cancer in asubject, the method comprising the steps of:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 4 markers in a population of the subject'smacrophage cells;

b) measuring the levels of the one or more selected Signature 4 markersin a population of the subject's non-phagocytic cells; and

c) identifying a difference between the measured levels of the one ormore selected Signature 4 markers in steps a) and b),

wherein the identified difference indicates that the subject has a riskof developing said prostate cancer.

21. A method for prognosing or aiding in the prognosis of prostatecancer in a subject, the method comprising the steps of:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 4 markers in a population of the subject'smacrophage cells;

b) measuring the levels of the one or more selected Signature 4 markersin a population of the subject's non-phagocytic cells; and

c) identifying a difference between the measured levels of the one ormore selected Signature 4 markers in steps a) and b),

wherein the identified difference is indicative of the prognosis of saidprostate cancer in the subject.

22. A method for assessing the efficacy of a treatment for prostatecancer in a subject comprising:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 4 markers in a population of the subject'smacrophage cells before the treatment;

b) measuring the levels of the one or more selected Signature 4 markersin a population of the subject's non-phagocytic cells before thetreatment;

c) identifying a first difference between the measured levels of the oneor more selected Signature 4 markers in steps a) and b);

d) measuring the levels of the one or more selected Signature 4 markersin a population of the subject's macrophage cells after the treatment;

e) measuring the levels of the one or more selected Signature 4 markersin a population of the subject's non-phagocytic cells after thetreatment;

f) identifying a second difference between the measured levels of theone or more selected Signature 4 markers in steps d) and e); and

g) identifying a difference between the first difference and the seconddifference,

wherein the difference identified in g) is indicative of the efficacy ofthe treatment for said prostate cancer in the subject.

23. A method for monitoring the progression or regression of prostatecancer in a subject comprising:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 4 markers in a population of the subject'smacrophage cells at a first time point;

b) measuring the levels of the one or more selected Signature 4 markersin a population of the subject's non-phagocytic cells at the first timepoint;

c) identifying a first difference between the measured levels of the oneor more selected Signature 4 markers in steps a) and b);

d) measuring the levels of the one or more selected Signature 4 markersin a population of the subject's macrophage cells at a second timepoint;

e) measuring the levels of the one or more selected Signature 4 markersin a population of the subject's non-phagocytic cells at the second timepoint;

f) identifying a second difference between the measured levels of theone or more selected Signature 4 markers in steps d) and e); and

g) identifying a difference between the first difference and the seconddifference,

wherein the difference identified in g) is indicative of the progressionor regression of said prostate cancer in the subject.

24. A method for identifying a compound capable of ameliorating ortreating prostate cancer in a subject comprising:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 4 markers in a population of the subject'smacrophage cells before administering the compound to the subject;

b) measuring the levels of the one or more selected Signature 4 markersin a population of the subject's non-phagocytic cells beforeadministering the compound to the subject;

c) identifying a first difference between the measured levels of the oneor more selected Signature 4 markers in steps a) and b);

d) measuring the levels of the one or more selected Signature 4 markersin a population of the subject's macrophage cells after theadministration of the compound;

e) measuring the levels of the one or more selected Signature 4 markersin a population of the subject's non-phagocytic cells after theadministration of the compound;

f) identifying a second difference between the measured levels of theone or more selected Signature 4 markers in steps d) and e); and

g) identifying a difference between the first difference and the seconddifference,

wherein the difference identified in g) indicates that the compound iscapable of ameliorating or treating said prostate cancer in the subject.

25. A method for diagnosing or aiding in the diagnosis of prostatecancer in a subject, the method comprising the steps of:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 1 markers in a population of the subject'sneutrophil cells;

b) measuring the levels of the one or more selected Signature 1 markersin a population of the subject's non-phagocytic cells; and

c) identifying a difference between the measured levels of the one ormore selected Signature 1 markers in steps a) and b),

wherein the identified difference indicates that the subject has saidprostate cancer.

26. A method for assessing the risk of developing prostate cancer in asubject, the method comprising the steps of:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 1 markers in a population of the subject'sneutrophil cells;

b) measuring the levels of the one or more selected Signature 1 markersin a population of the subject's non-phagocytic cells; and

c) identifying a difference between the measured levels of the one ormore selected Signature 1 markers in steps a) and b),

wherein the identified difference indicates that the subject has a riskof developing said prostate cancer.

27. A method for prognosing or aiding in the prognosis of prostatecancer in a subject, the method comprising the steps of:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 1 markers in a population of the subject'sneutrophil cells;

b) measuring the levels of the one or more selected Signature 1 markersin a population of the subject's non-phagocytic cells; and

c) identifying a difference between the measured levels of the one ormore selected Signature 1 markers in steps a) and b),

wherein the identified difference is indicative of the prognosis of saidprostate cancer in the subject.

28. A method for assessing the efficacy of a treatment for prostatecancer in a subject comprising:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 1 markers in a population of the subject'sneutrophil cells before the treatment;

b) measuring the levels of the one or more selected Signature 1 markersin a population of the subject's non-phagocytic cells before thetreatment;

c) identifying a first difference between the measured levels of the oneor more selected Signature 1 markers in steps a) and b);

d) measuring the levels of the one or more selected Signature 1 markersin a population of the subject's neutrophil cells after the treatment;

e) measuring the levels of the one or more selected Signature 1 markersin a population of the subject's non-phagocytic cells after thetreatment;

f) identifying a second difference between the measured levels of theone or more selected Signature 1 markers in steps d) and e); and

g) identifying a difference between the first difference and the seconddifference,

wherein the difference identified in g) is indicative of the efficacy ofthe treatment for said prostate cancer in the subject.

29. A method for monitoring the progression or regression of prostatecancer in a subject comprising:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 1 markers in a population of the subject'sneutrophil cells at a first time point;

b) measuring the levels of the one or more selected Signature 1 markersin a population of the subject's non-phagocytic cells at the first timepoint;

c) identifying a first difference between the measured levels of the oneor more selected Signature 1 markers in steps a) and b);

d) measuring the levels of the one or more selected Signature 1 markersin a population of the subject's neutrophil cells at a second timepoint;

e) measuring the levels of the one or more selected Signature 1 markersin a population of the subject's non-phagocytic cells at the second timepoint;

f) identifying a second difference between the measured levels of theone or more selected Signature 1 markers in steps d) and e); and

g) identifying a difference between the first difference and the seconddifference,

wherein the difference identified in g) is indicative of the progressionor regression of said prostate cancer in the subject.

30. A method for identifying a compound capable of ameliorating ortreating prostate cancer in a subject comprising:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 1 markers in a population of the subject'sneutrophil cells before administering the compound to the subject;

b) measuring the levels of the one or more selected Signature 1 markersin a population of the subject's non-phagocytic cells beforeadministering the compound to the subject;

c) identifying a first difference between the measured levels of the oneor more selected Signature 1 markers in steps a) and b);

d) measuring the levels of the one or more selected Signature 1 markersin a population of the subject's neutrophil cells after theadministration of the compound;

e) measuring the levels of the one or more selected Signature 1 markersin a population of the subject's non-phagocytic cells after theadministration of the compound;

f) identifying a second difference between the measured levels of theone or more selected Signature 1 markers in steps d) and e); and

g) identifying a difference between the first difference and the seconddifference,

wherein the difference identified in g) indicates that the compound iscapable of ameliorating or treating said prostate cancer in the subject.

31. A method for diagnosing or aiding in the diagnosis of prostatecancer in a subject, the method comprising the steps of:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 2 markers in a population of the subject'sneutrophil cells;

b) measuring the levels of the one or more selected Signature 2 markersin a population of the subject's non-phagocytic cells; and

c) identifying a difference between the measured levels of the one ormore selected Signature 2 markers in steps a) and b),

wherein the identified difference indicates that the subject has saidprostate cancer.

32. A method for assessing the risk of developing prostate cancer in asubject, the method comprising the steps of:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 2 markers in a population of the subject'sneutrophil cells;

b) measuring the levels of the one or more selected Signature 2 markersin a population of the subject's non-phagocytic cells; and

c) identifying a difference between the measured levels of the one ormore selected Signature 2 markers in steps a) and b),

wherein the identified difference indicates that the subject has a riskof developing said prostate cancer.

33. A method for prognosing or aiding in the prognosis of prostatecancer in a subject, the method comprising the steps of:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 2 markers in a population of the subject'sneutrophil cells;

b) measuring the levels of the one or more selected Signature 2 markersin a population of the subject's non-phagocytic cells; and

c) identifying a difference between the measured levels of the one ormore selected Signature 2 markers in steps a) and b),

wherein the identified difference is indicative of the prognosis of saidprostate cancer in the subject.

34. A method for assessing the efficacy of a treatment for prostatecancer in a subject comprising:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 2 markers in a population of the subject'sneutrophil cells before the treatment;

b) measuring the levels of the one or more selected Signature 2 markersin a population of the subject's non-phagocytic cells before thetreatment;

c) identifying a first difference between the measured levels of the oneor more selected Signature 2 markers in steps a) and b);

d) measuring the levels of the one or more selected Signature 2 markersin a population of the subject's neutrophil cells after the treatment;

e) measuring the levels of the one or more selected Signature 2 markersin a population of the subject's non-phagocytic cells after thetreatment;

f) identifying a second difference between the measured levels of theone or more selected Signature 2 markers in steps d) and e); and

g) identifying a difference between the first difference and the seconddifference,

wherein the difference identified in g) is indicative of the efficacy ofthe treatment for said prostate cancer in the subject.

35. A method for monitoring the progression or regression of prostatecancer in a subject comprising:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 2 markers in a population of the subject'sneutrophil cells at a first time point;

b) measuring the levels of the one or more selected Signature 2 markersin a population of the subject's non-phagocytic cells at the first timepoint;

c) identifying a first difference between the measured levels of the oneor more selected Signature 2 markers in steps a) and b);

d) measuring the levels of the one or more selected Signature 2 markersin a population of the subject's neutrophil cells at a second timepoint;

e) measuring the levels of the one or more selected Signature 2 markersin a population of the subject's non-phagocytic cells at the second timepoint;

f) identifying a second difference between the measured levels of theone or more selected Signature 2 markers in steps d) and e); and

g) identifying a difference between the first difference and the seconddifference,

wherein the difference identified in g) is indicative of the progressionor regression of said prostate cancer in the subject.

36. A method for identifying a compound capable of ameliorating ortreating prostate cancer in a subject comprising:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 2 markers in a population of the subject'sneutrophil cells before administering the compound to the subject;

b) measuring the levels of the one or more selected Signature 2 markersin a population of the subject's non-phagocytic cells beforeadministering the compound to the subject;

c) identifying a first difference between the measured levels of the oneor more selected Signature 2 markers in steps a) and b);

d) measuring the levels of the one or more selected Signature 2 markersin a population of the subject's neutrophil cells after theadministration of the compound;

e) measuring the levels of the one or more selected Signature 2 markersin a population of the subject's non-phagocytic cells after theadministration of the compound;

f) identifying a second difference between the measured levels of theone or more selected Signature 2 markers in steps d) and e); and

g) identifying a difference between the first difference and the seconddifference,

wherein the difference identified in g) indicates that the compound iscapable of ameliorating or treating said prostate cancer in the subject.

37. A method for diagnosing or aiding in the diagnosis of prostatecancer in a subject, the method comprising the steps of:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 3 markers in a population of the subject'sneutrophil cells;

b) measuring the levels of the one or more selected Signature 3 markersin a population of the subject's non-phagocytic cells; and

c) identifying a difference between the measured levels of the one ormore selected Signature 3 markers in steps a) and b),

wherein the identified difference indicates that the subject has saidprostate cancer.

38. A method for assessing the risk of developing prostate cancer in asubject, the method comprising the steps of:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 3 markers in a population of the subject'sneutrophil cells;

b) measuring the levels of the one or more selected Signature 3 markersin a population of the subject's non-phagocytic cells; and

c) identifying a difference between the measured levels of the one ormore selected Signature 3 markers in steps a) and b),

wherein the identified difference indicates that the subject has a riskof developing said prostate cancer.

39. A method for prognosing or aiding in the prognosis of prostatecancer in a subject, the method comprising the steps of:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 3 markers in a population of the subject'sneutrophil cells;

b) measuring the levels of the one or more selected Signature 3 markersin a population of the subject's non-phagocytic cells; and

c) identifying a difference between the measured levels of the one ormore selected Signature 3 markers in steps a) and b),

wherein the identified difference is indicative of the prognosis of saidprostate cancer in the subject.

40. A method for assessing the efficacy of a treatment for prostatecancer in a subject comprising:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 3 markers in a population of the subject'sneutrophil cells before the treatment;

b) measuring the levels of the one or more selected Signature 3 markersin a population of the subject's non-phagocytic cells before thetreatment;

c) identifying a first difference between the measured levels of the oneor more selected Signature 3 markers in steps a) and b);

d) measuring the levels of the one or more selected Signature 3 markersin a population of the subject's neutrophil cells after the treatment;

e) measuring the levels of the one or more selected Signature 3 markersin a population of the subject's non-phagocytic cells after thetreatment;

f) identifying a second difference between the measured levels of theone or more selected Signature 3 markers in steps d) and e); and

g) identifying a difference between the first difference and the seconddifference,

wherein the difference identified in g) is indicative of the efficacy ofthe treatment for said prostate cancer in the subject.

41. A method for monitoring the progression or regression of prostatecancer in a subject comprising:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 3 markers in a population of the subject'sneutrophil cells at a first time point;

b) measuring the levels of the one or more selected Signature 3 markersin a population of the subject's non-phagocytic cells at the first timepoint;

c) identifying a first difference between the measured levels of the oneor more selected Signature 3 markers in steps a) and b);

d) measuring the levels of the one or more selected Signature 3 markersin a population of the subject's neutrophil cells at a second timepoint;

e) measuring the levels of the one or more selected Signature 3 markersin a population of the subject's non-phagocytic cells at the second timepoint;

f) identifying a second difference between the measured levels of theone or more selected Signature 3 markers in steps d) and e); and

g) identifying a difference between the first difference and the seconddifference,

wherein the difference identified in g) is indicative of the progressionor regression of said prostate cancer in the subject.

42. A method for identifying a compound capable of ameliorating ortreating prostate cancer in a subject comprising:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 3 markers in a population of the subject'sneutrophil cells before administering the compound to the subject;

b) measuring the levels of the one or more selected Signature 3 markersin a population of the subject's non-phagocytic cells beforeadministering the compound to the subject;

c) identifying a first difference between the measured levels of the oneor more selected Signature 3 markers in steps a) and b);

d) measuring the levels of the one or more selected Signature 3 markersin a population of the subject's neutrophil cells after theadministration of the compound;

e) measuring the levels of the one or more selected Signature 3 markersin a population of the subject's non-phagocytic cells after theadministration of the compound;

f) identifying a second difference between the measured levels of theone or more selected Signature 3 markers in steps d) and e); and

g) identifying a difference between the first difference and the seconddifference,

wherein the difference identified in g) indicates that the compound iscapable of ameliorating or treating said prostate cancer in the subject.

43. A method for diagnosing or aiding in the diagnosis of prostatecancer in a subject, the method comprising the steps of:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 4 markers in a population of the subject'sneutrophil cells;

b) measuring the levels of the one or more selected Signature 4 markersin a population of the subject's non-phagocytic cells; and

c) identifying a difference between the measured levels of the one ormore selected Signature 4 markers in steps a) and b),

wherein the identified difference indicates that the subject has saidprostate cancer.

44. A method for assessing the risk of developing prostate cancer in asubject, the method comprising the steps of:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 4 markers in a population of the subject'sneutrophil cells;

b) measuring the levels of the one or more selected Signature 4 markersin a population of the subject's non-phagocytic cells; and

c) identifying a difference between the measured levels of the one ormore selected Signature 4 markers in steps a) and b),

wherein the identified difference indicates that the subject has a riskof developing said prostate cancer.

45. A method for prognosing or aiding in the prognosis of prostatecancer in a subject, the method comprising the steps of:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 4 markers in a population of the subject'sneutrophil cells;

b) measuring the levels of the one or more selected Signature 4 markersin a population of the subject's non-phagocytic cells; and

c) identifying a difference between the measured levels of the one ormore selected Signature 4 markers in steps a) and b),

wherein the identified difference is indicative of the prognosis of saidprostate cancer in the subject.

46. A method for assessing the efficacy of a treatment for prostatecancer in a subject comprising:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 4 markers in a population of the subject'sneutrophil cells before the treatment;

b) measuring the levels of the one or more selected Signature 4 markersin a population of the subject's non-phagocytic cells before thetreatment;

c) identifying a first difference between the measured levels of the oneor more selected Signature 4 markers in steps a) and b);

d) measuring the levels of the one or more selected Signature 4 markersin a population of the subject's neutrophil cells after the treatment;

e) measuring the levels of the one or more selected Signature 4 markersin a population of the subject's non-phagocytic cells after thetreatment;

f) identifying a second difference between the measured levels of theone or more selected Signature 4 markers in steps d) and e); and

g) identifying a difference between the first difference and the seconddifference,

wherein the difference identified in g) is indicative of the efficacy ofthe treatment for said prostate cancer in the subject.

47. A method for monitoring the progression or regression of prostatecancer in a subject comprising:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 4 markers in a population of the subject'sneutrophil cells at a first time point;

b) measuring the levels of the one or more selected Signature 4 markersin a population of the subject's non-phagocytic cells at the first timepoint;

c) identifying a first difference between the measured levels of the oneor more selected Signature 4 markers in steps a) and b);

d) measuring the levels of the one or more selected Signature 4 markersin a population of the subject's neutrophil cells at a second timepoint;

e) measuring the levels of the one or more selected Signature 4 markersin a population of the subject's non-phagocytic cells at the second timepoint;

f) identifying a second difference between the measured levels of theone or more selected Signature 4 markers in steps d) and e); and

g) identifying a difference between the first difference and the seconddifference,

wherein the difference identified in g) is indicative of the progressionor regression of said prostate cancer in the subject.

48. A method for identifying a compound capable of ameliorating ortreating prostate cancer in a subject comprising:

a) measuring the levels of one or more markers selected from the groupconsisting of Signature 4 markers in a population of the subject'sneutrophil cells before administering the compound to the subject;

b) measuring the levels of the one or more selected Signature 4 markersin a population of the subject's non-phagocytic cells beforeadministering the compound to the subject;

c) identifying a first difference between the measured levels of the oneor more selected Signature 4 markers in steps a) and b);

d) measuring the levels of the one or more selected Signature 4 markersin a population of the subject's neutrophil cells after theadministration of the compound;

e) measuring the levels of the one or more selected Signature 4 markersin a population of the subject's non-phagocytic cells after theadministration of the compound;

f) identifying a second difference between the measured levels of theone or more selected Signature 4 markers in steps d) and e); and

g) identifying a difference between the first difference and the seconddifference,

wherein the difference identified in g) indicates that the compound iscapable of ameliorating or treating said prostate cancer in the subject.

49. The method of any one of embodiments 1-48, further comprisingmeasuring at least one standard parameter associated with said prostatecancer.50. The method of embodiment 49, wherein the standard parameter isselected from the group consisting of tumor stage, tumor grade, tumorsize, tumor visual characteristics, tumor growth, tumor thickness, tumorprogression, tumor metastasis tumor distribution within the body, odor,molecular pathology, genomics, or tumor angiograms.51. The method of any one of embodiments 1-24, wherein the selectedSignature 1, Signature 2, Signature 3, or Signature 4 markers areup-regulated or activated in the macrophage cells compared to thenon-phagocytic cells.52. The method of any one of embodiments 1-24, wherein the selectedSignature 1, Signature 2, Signature 3, or Signature 4 markers aredown-regulated or inhibited in the macrophage cells compared to thenon-phagocytic cells.53. The method of any one of embodiments 1-24, wherein the selectedSignature 1, Signature 2, Signature 3, or Signature 4 markers areup-regulated or activated in the neutrophil cells compared to thenon-phagocytic cells.54. The method of any one of embodiments 1-24, wherein the selectedSignature 1, Signature 2, Signature 3, or Signature 4 markers aredown-regulated or inhibited in the neutrophil cells compared to thenon-phagocytic cells.55. The method of any one of embodiments 1-6 or 25-30, wherein at leasttwo, three, four, five, six, seven, eight, nine, ten, or eleven markersare selected from Signature 1.56. The method of any one of embodiments 7-12 or 31-36, wherein at leasttwo, three, four, five, six, seven, eight, nine, ten, or eleven markersare selected from Signature 2.57. The method of any one of embodiments 13-18 or 37-42, wherein atleast two, three, four, five, six, seven, eight, nine, ten, or elevenmarkers are selected from Signature 3.58. The method of any one of embodiments 19-24 or 43-48, wherein atleast two, three, four, five, six, seven, eight, nine, ten, or elevenmarkers are selected from Signature 4.59. The method of any one of embodiments 1-24, further comprising lysingthe macrophage cells and the non-phagocytic cells before a).60. The method of any one of embodiments 1-24, further comprisingextracting the cellular contents from the macrophage cells and thenon-phagocytic cells before a).61. The method of any one of embodiments 25-48, further comprisinglysing the neutrophil cells and the non-phagocytic cells before a).62. The method of any one of embodiments 25-48, further comprisingextracting the cellular contents from the neutrophil cells and thenon-phagocytic cells before a).63. The method of embodiment 60, wherein the cellular contents of themacrophage cells comprise viable diseased cells, dead diseased cells,apoptotic diseased cells, circulating tumor cells, infectious agents,fetal cells, trophoblasts, or fragments thereof64. The method of embodiment 62, wherein the cellular contents of theneutrophil cells comprise viable diseased cells, dead diseased cells,apoptotic diseased cells, circulating tumor cells, infectious agents,fetal cells, trophoblasts, or fragments thereof65. The method of embodiment 60, wherein the selected one or moremarkers are present in the cellular contents of the macrophage cells.66. The method of any one of embodiments 1-48, wherein thenon-phagocytic cells are T cells, B cells, null cells, basophils, ormixtures thereof67. The method of any one of embodiments 1-24, wherein the macrophagecells are isolated from a bodily fluid sample, tissues, or cells of thesubject.68. The method of any one of embodiments 25-48, wherein the neutrophilcells are isolated from a bodily fluid sample, tissues, or cells of thesubject.69. The method of any one of embodiments 1-48, wherein thenon-phagocytic cells are isolated from a bodily fluid sample, tissues,or cells of the subject.70. The method of any one of embodiments 67-69, wherein the bodily fluidsample is blood, urine, stool, saliva, lymph fluid, cerebrospinal fluid,synovial fluid, cystic fluid, ascites, pleural effusion, fluid obtainedfrom a pregnant woman in the first trimester, fluid obtained from apregnant woman in the second trimester, fluid obtained from a pregnantwoman in the third trimester, maternal blood, amniotic fluid, chorionicvillus sample, fluid from a preimplantation embryo, maternal urine,maternal saliva, placental sample, fetal blood, lavage and cervicalvaginal fluid, interstitial fluid, or ocular fluid.71. The method of any one of embodiments 1-24, wherein the macrophagecells are isolated using antibodies, using a ligand that binds to amolecular receptor expressed on the plasma membranes of white bloodcells, or by flow cytometry, fluorescence activated cell sorting,filtration, gradient-based centrifugation, elution, microfluidics,magnetic separation technique, fluorescent-magnetic separationtechnique, nanostructure, quantum dots, high throughput microscope-basedplatforms, or a combination thereof72. The method of any one of embodiments 25-48, wherein the neutrophilcells are isolated using antibodies, using a ligand that binds to amolecular receptor expressed on the plasma membranes of white bloodcells, or by flow cytometry, fluorescence activated cell sorting,filtration, gradient-based centrifugation, elution, microfluidics,magnetic separation technique, fluorescent-magnetic separationtechnique, nanostructure, quantum dots, high throughput microscope-basedplatforms, or a combination thereof73. The method of any one of embodiments 1-48, wherein thenon-phagocytic cells are isolated using antibodies, using a ligand thatbinds to a molecular receptor expressed on the plasma membranes of whiteblood cells, or by flow cytometry, fluorescence activated cell sorting,filtration, gradient-based centrifugation, elution, microfluidics,magnetic separation technique, fluorescent-magnetic separationtechnique, nanostructure, quantum dots, high throughput microscope-basedplatforms, or a combination thereof74. The method of any one of embodiments 1-24, wherein the macrophagecells are isolated using a product secreted by the macrophage cells.75. The method of any one of embodiments 25-48, wherein the neutrophilcells are isolated by using a product secreted by the neutrophil cells.76. The method of any one the embodiments 1-24, wherein the macrophagecells are isolated by using a cell surface target on the surface ofmacrophage cells.77. The method of any one of embodiments 25-48, wherein the neutrophilcells are isolated by using a cell surface target on the surface ofneutrophil cells.78. The method of embodiment 76, wherein the target is expressed by themacrophage cells.79. The method of embodiment 76, wherein the target is not expressed bythe macrophage cells.80. The method of embodiment 77, wherein the target is expressed by theneutrophil cells.81. The method of embodiment 77, wherein the target is not expressed bythe neutrophil cells.82. The method of any one of embodiments 76-81, wherein the target is amarker of said prostate cancer.83. The method of any one of embodiments 1-48, wherein the measuredlevels are gene expression levels.84. The method of any one of embodiments 1-48, wherein the measuredlevels are protein expression levels.85. The method of any one of the embodiment 1-48, wherein the levels oractivities are measured by a qualitative assay, a quantitative assay, ora combination thereof86. The method of embodiment 85, wherein the quantitative assay usessequencing, direct sequencing, RNA sequencing, whole transcriptomeshotgun sequencing, random shotgun sequencing, Sanger dideoxytermination sequencing, whole-genome sequencing, sequencing byhybridization, pyrosequencing, capillary electrophoresis, gelelectrophoresis, duplex sequencing, cycle sequencing, single-baseextension sequencing, solid-phase sequencing, high-throughputsequencing, massively parallel signature sequencing, emulsion PCR,sequencing by reversible dye terminator, paired-end sequencing,near-term sequencing, exonuclease sequencing, sequencing by ligation,short-read sequencing, single-molecule sequencing,sequencing-by-synthesis, real-time sequencing, reverse-terminatorsequencing, nanopore sequencing, 454 sequencing, Solexa Genome Analyzersequencing, SOLiD® sequencing, MS-PET sequencing, mass spectrometry,matrix assisted laser desorption/ionization-time of flight (MALDI-TOF)mass spectrometry, electrospray ionization (ESI) mass spectrometry,surface-enhanced laser desorption/ionization-time of flight (SELDI-TOF)mass spectrometry, quadrupole-time of flight (Q-TOF) mass spectrometry,atmospheric pressure photoionization mass spectrometry (APPI-MS),Fourier transform mass spectrometry (FTMS), matrix-assisted laserdesorption/ionization-Fourier transform-ion cyclotron resonance(MALDI-FT-ICR) mass spectrometry, secondary ion mass spectrometry(SIMS), polymerase chain reaction (PCR) analysis, quantitative PCR,real-time PCR, fluorescence assay, colorimetric assay, chemiluminescentassay, or a combination thereof.87. The method of embodiment 83, wherein the gene expression levels aremeasured by polymerase chain reaction (PCR) analysis, sequencinganalysis, electrophoretic analysis, restriction fragment lengthpolymorphism (RFLP) analysis, Northern blot analysis, quantitative PCR,reverse-transcriptase-PCR analysis (RT-PCR), allele-specificoligonucleotide hybridization analysis, comparative genomichybridization, heteroduplex mobility assay (HMA), single strandconformational polymorphism (SSCP), denaturing gradient gelelectrophisis (DGGE), RNAase mismatch analysis, mass spectrometry,tandem mass spectrometry, matrix assisted laserdesorption/ionization-time of flight (MALDI-TOF) mass spectrometry,electrospray ionization (ESI) mass spectrometry, surface-enhanced laserdeorption/ionization-time of flight (SELDI-TOF) mass spectrometry,quadrupole-time of flight (Q-TOF) mass spectrometry, atmosphericpressure photoionization mass spectrometry (APPI-MS), Fourier transformmass spectrometry (FTMS), matrix-assisted laserdesorption/ionization-Fourier transform-ion cyclotron resonance(MALDI-FT-ICR) mass spectrometry, secondary ion mass spectrometry(SIMS), surface plasmon resonance, Southern blot analysis, in situhybridization, fluorescence in situ hybridization (FISH), chromogenic insitu hybridization (CISH), immunohistochemistry (IHC), microarray,comparative genomic hybridization, karyotyping, multiplexligation-dependent probe amplification (MLPA), Quantitative MultiplexPCR of Short Fluorescent Fragments (QMPSF), microscopy, methylationspecific PCR (MSP) assay, HpaII tiny fragment Enrichment byLigation-mediated PCR (HELP) assay, radioactive acetate labeling assays,colorimetric DNA acetylation assay, chromatin immunoprecipitationcombined with microarray (ChIP-on-chip) assay, restriction landmarkgenomic scanning, Methylated DNA immunoprecipitation (MeDIP), molecularbreak light assay for DNA adenine methyltransferase activity,chromatographic separation, methylation-sensitive restriction enzymeanalysis, bisulfite-driven conversion of non-methylated cytosine touracil, methyl-binding PCR analysis, or a combination thereof88. The method of embodiment 83, wherein the gene expression levels aremeasured by a sequencing technique selected from the group consisting ofdirect sequencing, RNA sequencing, whole transcriptome shotgunsequencing, random shotgun sequencing, Sanger dideoxy terminationsequencing, whole-genome sequencing, sequencing by hybridization,pyrosequencing, capillary electrophoresis, gel electrophoresis, duplexsequencing, cycle sequencing, single-base extension sequencing,solid-phase sequencing, high-throughput sequencing, massively parallelsignature sequencing, emulsion PCR, sequencing by reversible dyeterminator, paired-end sequencing, near-term sequencing, exonucleasesequencing, sequencing by ligation, short-read sequencing,single-molecule sequencing, sequencing-by-synthesis, real-timesequencing, reverse-terminator sequencing, nanopore sequencing, 454sequencing, Solexa Genome Analyzer sequencing, SOLiD® sequencing, MS-PETsequencing, mass spectrometry, and a combination thereof89. The method of embodiment 84, wherein the protein expression levelsare measured by an immunohistochemistry assay, an enzyme-linkedimmunosorbent assay (ELISA), in situ hybridization, chromatography,liquid chromatography, size exclusion chromatography, high performanceliquid chromatography (HPLC), gas chromatography, mass spectrometry,tandem mass spectrometry, matrix assisted laserdesorption/ionization-time of flight (MALDI-TOF) mass spectrometry,electrospray ionization (ESI) mass spectrometry, surface-enhanced laserdeorption/ionization-time of flight (SELDI-TOF) mass spectrometry,quadrupole-time of flight (Q-TOF) mass spectrometry, atmosphericpressure photoionization mass spectrometry (APPI-MS), Fourier transformmass spectrometry (FTMS), matrix-assisted laserdesorption/ionization-Fourier transform-ion cyclotron resonance(MALDI-FT-ICR) mass spectrometry, secondary ion mass spectrometry(SIMS), radioimmunoassays, microscopy, microfluidic chip-based assays,surface plasmon resonance, sequencing, Western blotting assay, or acombination thereof.90. The method of any one the embodiments 1-89, wherein the subject is amammal.91. The method of embodiment 90, wherein the subject is a human.92. The method of any one the embodiments 1-48, wherein the differenceis greater than a 1-fold difference.93. The method of embodiment 92, wherein the difference is at least1.05-fold, 1.1-fold, 1.2-fold, 1.3-fold, 1.4-fold, 1.5-fold, 2-fold,2.5-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, or10-fold difference.94. A kit for measuring the levels of at least one or more markersselected from the group consisting of Signature 1 markers, comprisingreagents for specifically measuring the levels of the selected Signature1 marker.95. A kit for measuring the levels of at least one or more markersselected from the group consisting of Signature 2 markers, comprisingreagents for specifically measuring the levels of the selected Signature2 marker.96. A kit for measuring the levels of at least one or more markersselected from the group consisting of Signature 3 markers, comprisingreagents for specifically measuring the levels of the selected Signature3 marker.97. A kit for measuring the levels of at least one or more markersselected from the group consisting of Signature 4 markers, comprisingreagents for specifically measuring the levels of the selected Signature4 marker.98. The kit of any one of embodiments 95 and 96, wherein the reagentscomprise one or more antibodies or fragments thereof, oligonucleotides,or aptamers.99. A method of treating or preventing prostate cancer in a subjectcomprising administering to said subject an agent that modulates theactivity or expression of at least one or more markers selected from thegroup consisting of Signature 1.100. A method of treating or preventing prostate cancer in a subjectcomprising administering to said subject an agent that modulates theactivity or expression of at least one or more markers selected from thegroup consisting of Signature 2.101. A method of treating or preventing prostate cancer in a subjectcomprising administering to said subject an agent that modulates theactivity or expression of at least one or more markers selected from thegroup consisting of Signature 3.102. A method of treating or preventing prostate cancer in a subjectcomprising administering to said subject an agent that modulates theactivity or expression of at least one or more markers selected from thegroup consisting of Signature 4.103. The method of any one of embodiments 99-102, wherein the agent is asmall molecule modulator, siRNA, or an antibody or fragment thereof.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 depicts microarray results in a search for a signature of normal(N) vs. aggressive (A) cancer in subtraction-normalized expression datacollected from blood samples processed 4 hours after collection.

FIG. 2 depicts microarray results in search for a signature of normal(N) vs. aggressive (A) cancer in subtraction-normalized expression datacollected from blood samples processed 4 hours after collection. Theassay was used to search for stable transcripts (defined as those in thetop 1,000 differentially expressed genes, with subtraction normalizationat 4 hours) that had an expression level ratio of 0.8 to 1.25 in samplesprocessed 48 hours after collection compared to 4 hours aftercollection.

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides biological markers and methods of usingthem to detect a cancer. More specifically, the present inventionprovides biomarkers that are specific for prostate cancer.

As used here in, a “biomarker” or “marker” refers to an analyte (e.g., anucleic acid, DNA, RNA, peptide, protein, or metabolite) that can beobjectively measured and evaluated as an indicator for a biologicalprocess. In some embodiments, a marker is differentially detectable inphagocytes and is indicative of the presence or absence of prostatecancer. An analyte is differentially detectable if it can bedistinguished quantitatively or qualitatively in phagocytes compared toa control, e.g., a normal or healthy control or non-phagocytic cells.

The present invention is based on the discovery that one or more markersselected from Tables 1 and/or 2 and/or 3 and/or 4 (Signature 1 and/orSignature 2 and/or Signature 3 and/or Signature 4 markers, respectively)are useful in diagnosing prostate cancer. By measuring the levels of thebiomarkers (e.g., gene expression levels, protein expression levels, orprotein activity levels) in a population of phagocytes (e.g., macrophageor neutrophils) from a human subject, one can provide a reliablediagnosis for prostate cancer.

As used herein, a “level” of a marker of this invention can bequalitative (e.g., presence or absence) or quantitative (e.g., amounts,copy numbers, or dosages). In some embodiments, a level of a marker at azero value can indicate the absence of this marker. The levels of anymarker of this invention can be measured in various forms. For example,the level can be a gene expression level, a RNA transcript level, aprotein expression level, a protein activity level, an enzymaticactivity level.

The markers of this invention can be used in methods for diagnosing oraiding in the diagnosis of prostate cancer by comparing levels (e.g.,gene expression levels, or protein expression levels, or proteinactivities) of one or more prostate cancer markers (e.g., nucleic acidsor proteins) between phagocytes (e.g., macrophages or neutrophils) andnon-phagocytic cells taken from the same individual. This invention alsoprovides methods for assessing the risk of developing prostate cancer,prognosing said cancer, monitoring said cancer progression orregression, assessing the efficacy of a treatment, or identifying acompound capable of ameliorating or treating said cancer.

The methods of this invention can be applied to prostate cancer. As usedherein, “prostate cancer” means any cancer of the prostate including,but not limited to, adenocarcinoma and small cell carcinoma.

In a first aspect, the methods (e.g., diagnosis of prostate cancer,prognosis of prostate cancer, or assessing the risk of developingprostate cancer) provided in the invention comprise: a) measuring thelevels of one or more markers selected from Tables 1 and/or 2 and/or 3and/or 4 (Signature 1 markers and/or Signature 2 markers and/orSignature 3 markers and/or Signature 4 markers, respectively) in apopulation of a subject's macrophage cells; b) measuring the levels ofone or more of the selected markers in a population of a subject'snon-phagocytic cells (e.g., T-cells, B-cells, null cells, basophils orthe mixtures of two more non-phagocytic cells); comparing the measuredlevels in step a) to the measured levels in step b) and further identifya difference between the measured levels of a) and b). The identifieddifference is indicative of the diagnosis (e.g., presence or absence),prognosis (e.g., lethal outcome, or tumor stage), or the risk ofdeveloping prostate cancer.

In the first aspect, the selected markers comprise one or more (e.g.,two, three, four, five, six, seven, eight, nine, ten, twenty, thirty,forty, fifty, one-hundred, one-hundred seventeen, or any incrementbetween those values) markers of Signature 1, or one or more (e.g., two,three, four, five, six, seven, eight, nine, ten, eleven, twelve,thirteen, fourteen, fifteen, sixteen, seventeen, or eighteen) markers ofSignature 2, or one or more (e.g., two, two, three, four, five, six,seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen,sixteen, seventeen, or eighteen) markers of Signature 3, or one or more(e.g., two, two, three, four, five, six, seven, eight, nine, or ten)markers of Signature 4. In some embodiments, the selected markers areup-regulated (see Tables 1 and/or 2 and/or 3 and/or 4 for up-regulatedmarkers) in prostate cancer patients. In some embodiments, the selectedmarkers are down-regulated (see Table 1 for down-regulated markers) inprostate cancer patients. In some embodiments, the selected markerscomprise at least one Signature 1 marker that is up-regulated and atleast one Signature 1 marker that is down-regulated.

In a second aspect, the methods provided in this invention for assessingthe efficacy of a treatment for prostate cancer, monitoring theprogression or regression of prostate cancer, or identifying a compoundcapable of ameliorating or treating prostate cancer, respectively, in asubject comprising: a) measuring the levels of one or more markersselected from the group consisting of Signature 1 and/or Signature 2and/or Signature 3 and/or Signature 4 (Tables 1 and/or 2 and/or 3 and/or4, respectively) in a population of the subject's macrophage cellsbefore the treatment, or at a first time point, or before administrationof the compound, respectively; b) measuring the levels of the one ormore selected Signature 1 and/or Signature 2 and/or Signature 3 and/orSignature 4 markers in a population of the subject's non-phagocyticcells before the treatment, or at the first time point, or beforeadministration of the compound, respectively; c) identifying a firstdifference between the measured levels of the one or more selectedSignature 1 and/or Signature 2 and/or Signature 3 and/or Signature 4markers in steps a) and b); d) measuring the levels of the one or moreselected Signature 1 and/or

Signature 2 and/or Signature 3 and/or Signature 4 markers in apopulation of the subject's macrophage cells after the treatment, or ata second time point, or after administration of the compound,respectively; e) measuring the levels of the one or more selectedSignature 1 and/or Signature 2 and/or Signature 3 and/or Signature 4markers in a population of the subject's non-phagocytic cells after thetreatment, or at the second time point, or after administration of thecompound, respectively; f) identifying a second difference between themeasured levels of the one or more selected Signature 1 and/or Signature2 and/or Signature 3 and/or Signature 4 markers in steps d) and e); andg) identifying a difference between the first difference and the seconddifference, wherein the difference identified in g) is indicative of theefficacy of the treatment for the prostate cancer, or the progression orregression of the prostate cancer, or whether the compound is capable ofameliorating or treating the prostate cancer, respectively, in thesubject.

In a third aspect, the methods provided in this invention for assessingthe efficacy of a treatment for prostate cancer, monitoring theprogression or regression of prostate cancer, or identifying a compoundcapable of ameliorating or treating prostate cancer, respectively, in asubject comprising: a) measuring the levels of one or more markersselected from the group consisting of Signature 1 and/or Signature 2and/or Signature 3 and/or Signature 4 (Tables 1 and/or 2 and/or 3 and/or4, respectively) in a population of the subject's macrophage cellsbefore the treatment, or at a first time point, or before administrationof the compound, respectively; b) identifying a first difference betweenthe measured levels of the one or more selected Signature 1 and/orSignature 2 and/or Signature 3 and/or Signature 4 markers in step (a)and the levels of the one or more selected Signature 1 and/or Signature2 and/or Signature 3 and/or Signature 4 markers in a control (e.g., ahealthy control cell, or a control cell from a healthy subject) beforethe treatment, or at the first time point, or before administration ofthe compound, respectively; c) measuring the levels of the one or moreselected Signature 1 and/or Signature 2 and/or Signature 3 and/orSignature 4 markers in a population of the subject's macrophage cellsafter the treatment, or at a second time point, or after administrationof the compound, respectively; d) identifying a second differencebetween the measured levels of the one or more selected Signature 1and/or Signature 2 and/or Signature 3 and/or Signature 4 markers in stepc) and the levels of the one or more selected Signature 1 and/orSignature 2 and/or Signature 3 and/or Signature 4 markers in a controlafter the treatment, or at the second time point, or afteradministration of the compound, respectively; and e) identifying adifference between the first difference and the second difference,wherein the difference identified in e) is indicative of the efficacy ofthe treatment for the prostate cancer, or the progression or regressionof the prostate cancer, or whether the compound is capable ofameliorating or treating the prostate cancer, respectively, in thesubject.

In the second and third aspects, the selected markers comprise one ormore (e.g., two, three, four, five, six, seven, eight, nine, ten,twenty, thirty, forty, fifty, one-hundred, one-hundred seventeen, or anyincrement between those values) of Signature 1, or one or more (e.g.,two, three, four, five, six, seven, eight, nine, ten, eleven, twelve,thirteen, fourteen, fifteen, sixteen, seventeen, or eighteen) ofSignature 2, or one or more (e.g., two, two, three, four, five, six,seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen,sixteen, seventeen, or eighteen) markers of Signature 3, or one or more(e.g., two, two, three, four, five, six, seven, eight, nine, or ten)markers of Signature 4. In some embodiments, the selected markers areup-regulated (see Tables 1 and/or 2 and/or 3 and/or 4 for up-regulatedmarkers) in prostate cancer patients. In some embodiments, the selectedmarkers are down-regulated (see Table 1 for down-regulated markers) inprostate cancer patients. In some embodiments, the selected markerscomprise at least one Signature 1 marker that is up-regulated and atleast one Signature 1 marker that is down-regulated.

In some embodiments, two sub-populations of phagocytic cells are used inthe methods of this invention, i.e., phagocytic cells that have a DNAcontent greater than 2n (the >2n phagocytic cells) and phagocytic cellsthat have a DNA content of 2n (the =2n phagocytic cells). In thoseembodiments, the levels of the selected markers in the >2n phagocyticcells are compared to the =2n phagocytic cells to identify one or moredifference. The identified differences indicate whether the subject hasprostate cancer, or has a risk of developing prostate cancer, or has aprogressing or progressive prostate cancer.

In some embodiments, the levels of one or more markers from Tables 1 or2 or 3 or 4 are measured in combination with measuring the levels of oneor more markers from a different table from among Tables 1, 2, 3, and 4.

In various embodiments of the present invention, at least one or more ofthe selected markers (Signature 1 markers or Signature 2 markers orSignature 4 markers or Signature 4 markers) may be used in addition to abiological marker different from any of the selected markers. In someembodiments, such biological markers may be known markers for prostatecancer. In some embodiments, such biological markers and the substitutedselected markers may belong to the same signaling or biological pathway(e.g., a protein synthesis pathway, Th1 cytokine production pathway,transcription pathway, programmed cell death pathway), or may havesimilar biological function or activity (e.g., protein synthesis, Th1cytokine production, nucleotide binding, protein binding, transcription,a receptor for purines coupled to G-proteins, inhibition of programmedcell death, neutrophil activation, an IL-8 receptor, anHSP70-interacting protein, stimulating ATPase activity), or may beregulated by a common protein, or may belong to the same protein complex(e.g., an HSP70 protein complex).

In various embodiments of the present invention, a population of thesubject's macrophage cells is used as the selected phagocytic cells formeasuring the levels of the selected markers (e.g., Signature 1 and/orSignature 2 markers and/or Signature 3 markers and/or Signature 4markers) and a population of the subject's T-cells is used as theselected non-phagocytic cells for measuring the levels of the selectedmarkers (e.g., Signature 1 and/or Signature 2 markers and/or Signature 3markers and/or Signature 4 markers).

The gene names/descriptions provided in Tables 1 and 2 and 3 and 4 aremerely illustrative. The markers of this invention encompass all formsand variants of any specifically described markers, including, but notlimited to, polymorphic or allelic variants, isoforms, mutants,derivatives, precursors including nucleic acids and pro-proteins,cleavage products, and structures comprised of any of the markers asconstituent subunits of the fully assembled structure.

A “patient”, “subject”, or “individual” are used interchangeably andrefer to either a human or a non-human animal. These terms includemammals, such as humans, primates, livestock animals (e.g., bovines,porcines), companion animals (e.g., canines, felines) and rodents (e.g.,mice and rats).

As used herein, the terms “normal control”, “healthy control”, and“not-diseased cells” likewise mean a sample (e.g., cells, serum, tissue)taken from a source (e.g., subject, control subject, cell line) thatdoes not have the condition or disease being assayed and therefore maybe used to determine the baseline for the condition or disorder beingmeasured. A control subject refers to any individual that has not beendiagnosed as having the disease or condition being assayed. It is alsounderstood that the control subject, normal control, and healthycontrol, include data obtained and used as a standard, i.e. it can beused over and over again for multiple different subjects. In otherwords, for example, when comparing a subject sample to a control sample,the data from the control sample could have been obtained in a differentset of experiments, for example, it could be an average obtained from anumber of healthy subjects and not actually obtained at the time thedata for the subject was obtained.

The term “diagnosis” as used herein refers to methods by which theskilled artisan can estimate and/or determine whether or not a patientis suffering from a given disease or condition. In some embodiments, theterm “diagnosis” also refers to staging (e.g., Stage I, II, III, or IV)of cancer. The skilled artisan often makes a diagnosis on the basis ofone or more diagnostic indicators, e.g., a marker, the presence,absence, amount, or change in amount of which is indicative of thepresence, severity, or absence of the condition.

The term “prognosis” as used herein refers to is used herein to refer tothe likelihood of prostate cancer progression, including recurrence ofprostate cancer, and/or evaluation of whether the prostate cancer isaggressive or indolent.

The disclosure of the International Applications PCT/US11/44969,PCT/US11/45018, and PCT/US09/31395 and U.S. Provisional Applications61/660,518 and 61/660,427 are incorporated herein by reference for allpurposes.

Each embodiment described herein may be combined with any otherembodiment described herein.

Methods using the prostate cancer markers described herein provide highspecificity, sensitivity, and accuracy in detecting and diagnosingprostate cancer. The methods also eliminate the “inequality of baseline”that is known to occur among individuals due to intrinsic (e.g., age,gender, ethnic background, health status and the like) and temporalvariations in marker expression. Additionally, by using a comparison ofphagocytes and non-phagocytes from the same individual, the methods alsoallow detection, diagnosis, and treatment to be personalized to theindividual. Accordingly, in some embodiments, the invention providesnon-invasive assays for the early detection of prostate cancer, i.e.,before the prostate cancer can be diagnosed by conventional diagnostictechniques, e.g., imaging techniques, and, therefore, provide afoundation for improved decision-making relative to the needs andstrategies for intervention, prevention, and treatment of individualswith such disease or condition.

The methods described herein are supported by whole genome microarraydata of total RNA samples isolated from macrophages and fromnon-phagocytic T cells. The samples were obtained from human subjectswith and without prostate cancer. The data from these microarrayexperiments demonstrate that macrophage-T cell comparisons easily andaccurately differentiate between prostate cancer patients and humansubjects without prostate cancer.

The methods of this invention can be used together with any knowndiagnostic methods, such as physical inspection, visual inspection,biopsy, scanning, histology, radiology, imaging, ultrasound, use of acommercial kit, genetic testing, immunological testing, analysis ofbodily fluids, or monitoring neural activity.

Phagocytic cells that can be used in the methods of this inventioninclude all types of cells that are capable of ingesting various typesof substances (e.g., apoptotic cells, infectious agents, dead cells,viable cells, cell-free DNAs, cell-free RNAs, cell-free proteins). Insome embodiments, the phagocytic cells are neutrophils, macrophages,monocytes, dendritic cells, foam cells, mast cells, eosinophils, orkeratinocytes. In some embodiments, the phagocytic cells can be amixture of different types of phagocytic cells. In some embodiments, thephagocytic cells can be activated phagocytic cells, e.g., activatedmacrophages or neutrophils. In some embodiments, a phagocyte is ahistiocyte, e.g., a Langerhans cell.

As used herein, “treating” prostate cancer refers to taking steps toobtain beneficial or desired results, including clinical results.Beneficial or desired clinical results include, but are not limited to,alleviation or amelioration of one or more symptoms associated withdiseases or conditions.

As used herein, “administering” or “administration of” a compound or anagent to a subject can be carried out using one of a variety of methodsknown to those skilled in the art. For example, a compound or an agentcan be administered, intravenously, arterially, intradermally,intramuscularly, intraperitonealy, intravenously, subcutaneously,ocularly, sublingually, orally (by ingestion), intranasally (byinhalation), intraspinally, intracerebrally, and transdermally (byabsorption, e.g., through a skin duct). A compound or agent can alsoappropriately be introduced by rechargeable or biodegradable polymericdevices or other devices, e.g., patches and pumps, or formulations,which provide for the extended, slow, or controlled release of thecompound or agent. Administering can also be performed, for example,once, a plurality of times, and/or over one or more extended periods. Insome aspects, the administration includes both direct administration,including self-administration, and indirect administration, includingthe act of prescribing a drug. For example, as used herein, a physicianwho instructs a patient to self-administer a drug, or to have the drugadministered by another and/or who provides a patient with aprescription for a drug is administering the drug to the patient. Insome embodiments, a compound or an agent is administered orally, e.g.,to a subject by ingestion, or intravenously, e.g., to a subject byinjection. In some embodiments, the orally administered compound oragent is in an extended release or slow release formulation, oradministered using a device for such slow or extended release.

In certain embodiments, markers used in the methods of invention areup-regulated or activated in phagocytes (e.g., macrophages orneutrophils) compared to non-phagocytes. In certain embodiments, markersused in the methods of invention are down-regulated or inhibited inphagocytes (e.g., macrophages or neutrophils) compared tonon-phagocytes. As used herein, “up-regulation or up-regulated” canrefer to an increase in expression levels (e.g., gene expression orprotein expression), gene copy numbers, gene dosages, and otherqualitative or quantitative detectable state of the markers. Similarly,“down-regulation or down-regulated” can refer to a decrease inexpression levels, gene copy numbers, gene dosages, and otherqualitative or quantitative detectable state of the markers. As usedherein, “activation or activated” can refer to an active state of themarker, e.g., a phosphorylation state, a DNA methylation state, or a DNAacetylation state. Similarly, “inhibition or inhibited” can refer to arepressed state or an inactivated state of the marker, e.g., ade-phosphorylation state, a ubiquitination state, or a DNAde-methylation state.

In certain embodiments, methods of this invention also comprise at leastone of the following steps before determination of various levels: i)lysing the phagocytic or non-phagocytic cells; and ii) extractingcellular contents from the lysed cells. Any known cell lysis andextraction methods can be used herein. In certain embodiments, at leastone or more prostate cancer markers are present in the phagocytes. Incertain embodiments, there is no marker present in the cellular contentsof the non-phagocytic cells.

In certain embodiments, the phagocytic cells and/or non-phagocytic cellsare isolated from a bodily fluid sample, tissues, or population ofcells. Exemplary bodily fluid samples can be whole blood, urine, stool,saliva, lymph fluid, cerebrospinal fluid, synovial fluid, cystic fluid,ascites, pleural effusion, fluid obtained from a pregnant woman in thefirst trimester, fluid obtained from a pregnant woman in the secondtrimester, fluid obtained from a pregnant woman in the third trimester,maternal blood, amniotic fluid, chorionic villus sample, fluid from apreimplantation embryo, maternal urine, maternal saliva, placentalsample, fetal blood, lavage and cervical vaginal fluid, interstitialfluid, buccal swab sample, sputum, bronchial lavage, Pap smear sample,or ocular fluid. In some embodiments, the phagocytic cells ornon-phagocytic cells are isolated from white blood cells.

In the methods of this invention, cell separation/isolation/purificationmethods are used to isolate populations of cells from bodily fluidsample, cells, or tissues of a subject. A skilled worker can use anyknown cell separation/isolation/purification techniques to isolatephagocytic cells and non-phagocytic cells from a bodily fluid. Exemplarytechniques include, but are not limited to, using antibodies, flowcytometry, fluorescence activated cell sorting, filtration,gradient-based centrifugation, elution, microfluidics, magneticseparation technique, fluorescent-magnetic separation technique,nanostructure, quantum dots, high throughput microscope-based platform,or a combination thereof

In certain embodiments, the phagocytic cells and/or non-phagocytic cellsare isolated by using a product secreted by the cells. In certainembodiments, the phagocytic cells and/or non-phagocytic cells areisolated by using a cell surface target (e.g., receptor protein) on thesurface of the cells. In some embodiments, the cell surface target is aprotein that has been engulfed by phagocytic cells. In some embodiments,the cell surface target is expressed by cells on their plasma membranes.In some embodiments, the cell surface target is an exogenous proteinthat is translocated on the plasma membranes, but not expressed by thecells (e.g., the phagocytic cells). In some embodiments, the cellsurface target is a marker of prostate cancer.

In certain aspects of the methods described herein, analytes includenucleic acids, proteins, or any combinations thereof. In certain aspectsof the methods described herein, markers include nucleic acids,proteins, or any combinations thereof. As used herein, the term “nucleicacid” is intended to include DNA molecules (e.g., cDNA or genomic DNA),RNA molecules (e.g., mRNA), DNA-RNA hybrids, and analogs of the DNA orRNA generated using nucleotide analogs. The nucleic acid molecule can bea nucleotide, oligonucleotide, double-stranded DNA, single-stranded DNA,multi-stranded DNA, complementary DNA, genomic DNA, non-coding DNA,messenger RNA (mRNAs), microRNA (miRNAs), small nucleolar RNA (snoRNAs),ribosomal RNA (rRNA), transfer RNA (tRNA), small interfering RNA(siRNA), heterogeneous nuclear RNAs (hnRNA), or small hairpin RNA(shRNA). In some embodiments, the nucleic acid is a transrenal nucleicacid. A transrenal nucleic acid is an extracellular nucleic acid that isexcreted in the urine. See, e.g., U.S. Patent Publication No.20100068711 and U.S. Patent Publication No. 20120021404.

As used herein, the term “amino acid” includes organic compoundscontaining both a basic amino group and an acidic carboxyl group.Included within this term are natural amino acids (e.g., L-amino acids),modified and unusual amino acids (e.g., D-amino acids and β-aminoacids), as well as amino acids which are known to occur biologically infree or combined form but usually do not occur in proteins. Naturalprotein occurring amino acids include alanine, arginine, asparagine,aspartic acid, cysteine, glutamic acid, glutamine, glycine, histidine,isoleucine, leucine, lysine, methionine, phenylalanine, serine,threonine, tyrosine, tryptophan, proline, and valine. Naturalnon-protein amino acids include arginosuccinic acid, citrulline,cysteine sulfuric acid, 3,4-dihydroxyphenylalanine, homocysteine,homoserine, ornithine, 3-monoiodotyrosine, 3,5-diiodotryosine, 3, 5,5-triiodothyronine, and 3,3′,5,5′-tetraiodothyronine. Modified orunusual amino acids include D-amino acids, hydroxylysine,4-hydroxyproline, N-Cbz-protected amino acids, 2,4-diaminobutyric acid,homoarginine, norleucine, N-methylaminobutyric acid, naphthylalanine,phenylglycine, α-phenylproline, tert-leucine, 4-aminocyclohexylalanine,N-methyl-norleucine, 3,4-dehydroproline, N,N-dimethylaminoglycine,N-methylaminoglycine, 4-aminopiperidine-4-carboxylic acid,6-aminocaproic acid, trans-4-(aminomethyl)-cyclohexanecarboxylic acid,2-, 3-, and 4-(aminomethyl)-benzoic acid, 1-aminocyclopentanecarboxylicacid, 1-aminocyclopropanecarboxylic acid, and 2-benzyl-5-aminopentanoicacid.

As used herein, the term “peptide” includes compounds that consist oftwo or more amino acids that are linked by means of a peptide bond.Peptides may have a molecular weight of less than 10,000 Daltons, lessthan 5,000 Daltons, or less than 2,500 Daltons. The term “peptide” alsoincludes compounds containing both peptide and non-peptide components,such as pseudopeptide or peptidomimetic residues or other non-amino acidcomponents. Such compounds containing both peptide and non-peptidecomponents may also be referred to as a “peptide analog.”

As used herein, the term “protein” includes compounds that consist ofamino acids arranged in a linear chain and joined together by peptidebonds between the carboxyl and amino groups of adjacent amino acidresidues. Proteins used in methods of the invention include, but are notlimited to, amino acids, peptides, antibodies, antibody fragments,cytokines, lipoproteins, or glycoproteins.

As used herein, the term “antibody” includes polyclonal antibodies,monoclonal antibodies (including full length antibodies which have animmunoglobulin Fc region), antibody compositions with polyepitopicspecificity, multispecific antibodies (e.g., bispecific antibodies,diabodies, and single-chain molecules, and antibody fragments (e.g., Fabor F(ab′)₂, and Fv). For the structure and properties of the differentclasses of antibodies, see e.g., Basic and Clinical Immunology, 8thEdition, Daniel P. Sties, Abba I. Ten and Tristram G. Parsolw (eds),Appleton & Lange, Norwalk, Conn., 1994, page 71 and Chapter 6.

As used herein, the term “cytokine” refers to a secreted protein oractive fragment or mutant thereof that modulates the activity of cellsof the immune system. Examples of cytokines include, without limitation,interleukins, interferons, chemokines, tumor necrosis factors,colony-stimulating factors for immune cell precursors, and the like.

As used herein, the term “lipoprotein” includes negatively chargedcompositions that comprise a core of hydrophobic cholesteryl esters andtriglyceride surrounded by a surface layer of amphipathic phospholipidswith which free cholesterol and apolipoproteins are associated.Lipoproteins may be characterized by their density (e.g.very-low-density lipoprotein (VLDL), low-density lipoprotein (LDL) andhigh density lipoprotein (HDL)), which is determined by their size, therelative amounts of lipid and protein. Lipoproteins may also becharacterized by the presence or absence of particular modifications(e.g. oxidization, acetylation, or glycation).

As used herein, the term “glycoprotein” includes glycosides which haveone or more oligo- or polysaccharides covalently attached to a peptideor protein. Exemplary glycoproteins can include, without limitation,immunoglobulins, members of the major histocompatibility complex,collagens, mucins, glycoprotein IIb/IIIa, glycoprotein-41 (gp41) andglycoprotein-120 (gp12), follicle-stimulating hormone,alpha-fetoprotein, erythropoietin, transferrins, alkaline phosphatase,and lectins.

In some embodiments of the invention, a sample may comprise one or morestabilizers for a cell or an analyte such as DNA, RNA, and/or protein.For example, a sample may comprise a DNA stabilizer, an RNA stabilizer,and/or a protein stabilizer. Stabilizers are well known in the art andinclude, for example, DNAse inhibitors, RNAse inhibitors, and proteaseinhibitors or equivalents thereof

In some embodiments of the invention, levels of at least one or moreprostate cancer markers are compared. This comparison can bequantitative or qualitative. Quantitative measurements can be takenusing any of the assays described herein. For example, sequencing,direct sequencing, random shotgun sequencing, Sanger dideoxy terminationsequencing, targeted sequencing, whole-genome sequencing, sequencing byhybridization, pyrosequencing, capillary electrophoresis, gelelectrophoresis, duplex sequencing, cycle sequencing, single-baseextension sequencing, solid-phase sequencing, high-throughputsequencing, massively parallel signature sequencing, emulsion PCR,co-amplification at lower denaturation temperature-PCR (COLD-PCR),sequencing by reversible dye terminator, paired-end sequencing,near-term sequencing, exonuclease sequencing, sequencing by ligation,short-read sequencing, single-molecule sequencing,sequencing-by-synthesis, real-time sequencing, reverse-terminatorsequencing, nanopore sequencing, 454 sequencing, Solexa Genome Analyzersequencing, SOLiD® sequencing, MS-PET sequencing, mass spectrometry,matrix assisted laser desorption/ionization-time of flight (MALDI-TOF)mass spectrometry, electrospray ionization (ESI) mass spectrometry,surface-enhanced laser deorption/ionization-time of flight (SELDI-TOF)mass spectrometry, quadrupole-time of flight (Q-TOF) mass spectrometry,atmospheric pressure photoionization mass spectrometry (APPI-MS),Fourier transform mass spectrometry (FTMS), matrix-assisted laserdesorption/ionization-Fourier transform-ion cyclotron resonance(MALDI-FT-ICR) mass spectrometry, secondary ion mass spectrometry(SIMS), polymerase chain reaction (PCR) analysis, quantitative PCR,real-time PCR, fluorescence assay, colorimetric assay, chemiluminescentassay, or a combination thereof.

Quantitative comparisons can include statistical analyses such ast-test, ANOVA, Krustal-Wallis, Wilcoxon, Mann-Whitney, and odds ratio.Quantitative differences can include differences in the levels ofmarkers between levels or differences in the numbers of markers presentbetween levels, and combinations thereof. Examples of levels of themarkers can be, without limitation, gene expression levels, nucleic acidlevels, and protein levels. Qualitative differences can include, but arenot limited to, activation and inactivation, protein degradation,nucleic acid degradation, and covalent modifications.

In certain embodiments of the invention, the level is a nucleic acidlevel or a protein level, or a combination thereof. The level can bequalitatively or quantitatively determined.

A nucleic acid level can be, without limitation, a genotypic level, asingle nucleotide polymorphism level, a gene mutation level, a gene copynumber level, a DNA methylation level, a DNA acetylation level, achromosome dosage level, a gene expression level, or a combinationthereof.

The nucleic acid level can be determined by any methods known in the artto detect genotypes, single nucleotide polymorphisms, gene mutations,gene copy numbers, DNA methylation states, DNA acetylation states,chromosome dosages. Exemplary methods include, but are not limited to,polymerase chain reaction (PCR) analysis, sequencing analysis,electrophoretic analysis, restriction fragment length polymorphism(RFLP) analysis, Northern blot analysis, quantitative PCR,reverse-transcriptase-PCR analysis (RT-PCR), allele-specificoligonucleotide hybridization analysis, comparative genomichybridization, heteroduplex mobility assay (HMA), single strandconformational polymorphism (SSCP), denaturing gradient gelelectrophisis (DGGE), RNAase mismatch analysis, mass spectrometry,tandem mass spectrometry, matrix assisted laserdesorption/ionization-time of flight (MALDI-TOF) mass spectrometry,electrospray ionization (ESI) mass spectrometry, surface-enhanced laserdeorption/ionization-time of flight (SELDI-TOF) mass spectrometry,quadrupole-time of flight (Q-TOF) mass spectrometry, atmosphericpressure photoionization mass spectrometry (APPI-MS), Fourier transformmass spectrometry (FTMS), matrix-assisted laserdesorption/ionization-Fourier transform-ion cyclotron resonance(MALDI-FT-ICR) mass spectrometry, secondary ion mass spectrometry(SIMS), surface plasmon resonance, Southern blot analysis, in situhybridization, fluorescence in situ hybridization (FISH), chromogenic insitu hybridization (CISH), immunohistochemistry (IHC), microarray,comparative genomic hybridization, karyotyping, multiplexligation-dependent probe amplification (MLPA), Quantitative MultiplexPCR of Short Fluorescent Fragments (QMPSF), microscopy, methylationspecific PCR (MSP) assay, HpaII tiny fragment Enrichment byLigation-mediated PCR (HELP) assay, radioactive acetate labeling assays,colorimetric DNA acetylation assay, chromatin immunoprecipitationcombined with microarray (ChIP-on-chip) assay, restriction landmarkgenomic scanning, Methylated DNA immunoprecipitation (MeDIP), molecularbreak light assay for DNA adenine methyltransferase activity,chromatographic separation, methylation-sensitive restriction enzymeanalysis, bisulfite-driven conversion of non-methylated cytosine touracil, co-amplification at lower denaturation temperature-PCR(COLD-PCR), multiplex PCR, methyl-binding PCR analysis, or a combinationthereof

As used herein, the term “sequencing” is used in a broad sense andrefers to any technique known in the art that allows the order of atleast some consecutive nucleotides in at least part of a nucleic acid tobe identified, including without limitation at least part of anextension product or a vector insert. Exemplary sequencing techniquesinclude targeted sequencing, single molecule real-time sequencing, wholetranscriptome shotgun sequencing (“RNA-seq”), electron microscopy-basedsequencing, transistor-mediated sequencing, direct sequencing, randomshotgun sequencing, Sanger dideoxy termination sequencing, exonsequencing, whole-genome sequencing, sequencing by hybridization,pyrosequencing, capillary electrophoresis, gel electrophoresis, duplexsequencing, cycle sequencing, single-base extension sequencing,solid-phase sequencing, high-throughput sequencing, massively parallelsignature sequencing, emulsion PCR, co-amplification at lowerdenaturation temperature-PCR (COLD-PCR), multiplex PCR, sequencing byreversible dye terminator, paired-end sequencing, near-term sequencing,exonuclease sequencing, sequencing by ligation, short-read sequencing,single-molecule sequencing, sequencing-by-synthesis, real-timesequencing, reverse-terminator sequencing, nanopore sequencing, 454sequencing, Solexa Genome Analyzer sequencing, SOLiD® sequencing, MS-PETsequencing, mass spectrometry, and a combination thereof. In someembodiments, sequencing comprises an detecting the sequencing productusing an instrument, for example but not limited to an ABI PRISM® 377DNA Sequencer, an ABI PRISM® 310, 3100, 3100-Avant, 3730, or 373OxIGenetic Analyzer, an ABI PRISM® 3700 DNA Analyzer, or an AppliedBiosystems SOLiD™ System (all from Applied Biosystems), a GenomeSequencer 20 System (Roche Applied Science), or a mass spectrometer. Incertain embodiments, sequencing comprises emulsion PCR. In certainembodiments, sequencing comprises a high throughput sequencingtechnique, for example but not limited to, massively parallel signaturesequencing (MPSS).

In further embodiments of the invention, a protein level can be aprotein expression level, a protein activation level, or a combinationthereof. In some embodiments, a protein activation level can comprisedetermining a phosphorylation state, an ubiquitination state, amyristoylation state, or a conformational state of the protein.

A protein level can be detected by any methods known in the art fordetecting protein expression levels, protein phosphorylation state,protein ubiquitination state, protein myristoylation state, or proteinconformational state. In some embodiments, a protein level can bedetermined by an immunohistochemistry assay, an enzyme-linkedimmunosorbent assay (ELISA), in situ hybridization, chromatography,liquid chromatography, size exclusion chromatography, high performanceliquid chromatography (HPLC), gas chromatography, mass spectrometry,tandem mass spectrometry, matrix assisted laserdesorption/ionization-time of flight (MALDI-TOF) mass spectrometry,electrospray ionization (ESI) mass spectrometry, surface-enhanced laserdeorption/ionization-time of flight (SELDI-TOF) mass spectrometry,quadrupole-time of flight (Q-TOF) mass spectrometry, atmosphericpressure photoionization mass spectrometry (APPI-MS), Fourier transformmass spectrometry (FTMS), matrix-assisted laserdesorption/ionization-Fourier transform-ion cyclotron resonance(MALDI-FT-ICR) mass spectrometry, secondary ion mass spectrometry(SIMS), radioimmunoassays, microscopy, microfluidic chip-based assays,surface plasmon resonance, sequencing, Western blotting assay, or acombination thereof.

As used herein, the “difference” between different levels detected bythe methods of this invention can refer to different gene copy numbers,different DNA, RNA, or protein expression levels, different DNAmethylation states, different DNA acetylation states, and differentprotein modification states. The difference can be a difference greaterthan 1 fold. In some embodiments, the difference is a 1.05-fold,1.1-fold, 1.2-fold, 1.3-fold, 1.4-fold, 1.5-fold, 2-fold, 2.5-fold,3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, or 10-folddifference. In some embodiments, the difference is any fold differencebetween 1-10, 2-10, 5-10, 10-20, or 10-100 fold.

In some embodiments, the difference is differential gene expression(DGE), e.g. DGE of phagocytes vs. non-phagocytes. DGE can be measured asX=log₂(Y_(P))−log₂(Y_(NP)). The DGE may be any number, provided that itis significantly different between the phagocytes and thenon-phagocytes. For example, a 2-fold increased in gene expression couldbe represented asX=log₂(Y_(P))−log₂(Y_(NP))=log₂(Y_(P)/Y_(NP))=log₂(2)=1, while a 2-folddecrease in gene expression could be represented asX=log₂(Y_(P))−log₂(Y_(NP))=log₂(Y_(P)/Y_(NP))=log₂(½)=−1. Down-regulatedgenes have X<0, while up-regulated genes have X>0. See, e.g., Efron, JAm Stat Assoc 104:1015-1028 (2009).

A general principle of assays to detect markers involves preparing asample or reaction mixture that may contain the marker (e.g., one ormore of DNA, RNA, or protein) and a probe under appropriate conditionsand for a time sufficient to allow the marker and probe to interact andbind, thus forming a complex that can be removed and/or detected in thereaction mixture. These assays can be conducted in a variety of ways.

For example, one method to conduct such an assay would involve anchoringthe marker or probe onto a solid phase support, also referred to as asubstrate, and detecting target marker/probe complexes anchored on thesolid phase at the end of the reaction. In one embodiment of such amethod, a sample from a subject, which is to be assayed for presenceand/or concentration of marker, can be anchored onto a carrier or solidphase support. In another embodiment, the reverse situation is possible,in which the probe can be anchored to a solid phase and a sample from asubject can be allowed to react as an unanchored component of the assay.

There are many established methods for anchoring assay components to asolid phase. These include, without limitation, marker or probemolecules which are immobilized through conjugation of biotin andstreptavidin. Such biotinylated assay components can be prepared frombiotin-NHS(N-hydroxy-succinimide) using techniques known in the art(e.g., biotinylation kit, Pierce Chemicals, Rockford, Ill.), andimmobilized in the wells of streptavidin-coated 96 well plates (PierceChemical). In certain embodiments, the surfaces with immobilized assaycomponents can be prepared in advance and stored.

Other suitable carriers or solid phase supports for such assays includeany material capable of binding the class of molecule to which themarker or probe belongs. Well known supports or carriers include, butare not limited to, glass, polystyrene, nylon, polypropylene, nylon,polyethylene, dextran, amylases, natural and modified celluloses,polyacrylamides, gabbros, and magnetite.

In order to conduct assays with the above mentioned approaches, thenon-immobilized component is added to the solid phase upon which thesecond component is anchored. After the reaction is complete,uncomplexed components may be removed (e.g., by washing) underconditions such that any complexes formed will remain immobilized uponthe solid phase. The detection of marker/probe complexes anchored to thesolid phase can be accomplished in a number of methods outlined herein.

In certain exemplary embodiments, the probe, when it is the unanchoredassay component, can be labeled for the purpose of detection and readoutof the assay, either directly or indirectly, with detectable labelsdiscussed herein and which are well-known to one skilled in the art.

It is also possible to directly detect marker/probe complex formationwithout further manipulation or labeling of either component (marker orprobe), for example by utilizing the technique of fluorescence energytransfer (see, for example, U.S. Pat. Nos. 5,631,169 and 4,868,103). Afluorophore label on the first, ‘donor’ molecule is selected such that,upon excitation with incident light of appropriate wavelength, itsemitted fluorescent energy will be absorbed by a fluorescent label on asecond ‘acceptor’ molecule, which in turn is able to fluoresce due tothe absorbed energy. Alternately, the ‘donor’ protein molecule maysimply utilize the natural fluorescent energy of tryptophan residues.Labels are chosen that emit different wavelengths of light, such thatthe ‘acceptor’ molecule label may be differentiated from that of the‘donor’. Since the efficiency of energy transfer between the labels isrelated to the distance separating the molecules, spatial relationshipsbetween the molecules can be assessed. In a situation in which bindingoccurs between the molecules, the fluorescent emission of the ‘acceptor’molecule label in the assay should be maximal. A FRET binding event canbe conveniently measured through standard fluorometric detection meanswell known in the art (e.g., using a fluorimeter).

In another embodiment, determination of the ability of a probe torecognize a marker can be accomplished without labeling either assaycomponent (probe or marker) by utilizing a technology such as real-timeBiomolecular Interaction Analysis (BIA) (see, e.g., Sjolander, S. andUrbaniczky, C, 1991, Anal. Chem. 63:2338 2345 and Szabo et al, 1995,Curr. Opin. Struct. Biol. 5:699 705). As used herein, “BIA” or “surfaceplasmon resonance” is a technology for studying biospecific interactionsin real time, without labeling any of the interactants (e.g., BIAcore).Changes in the mass at the binding surface (indicative of a bindingevent) result in alterations of the refractive index of light near thesurface (the optical phenomenon of surface plasmon resonance (SPR)),resulting in a detectable signal which can be used as an indication ofreal-time reactions between biological molecules.

Alternatively, in another embodiment, analogous diagnostic andprognostic assays can be conducted with marker and probe as solutes in aliquid phase. In such an assay, the complexed marker and probe areseparated from uncomplexed components by any of a number of standardtechniques, including but not limited to: differential centrifugation,chromatography, electrophoresis and immunoprecipitation. In differentialcentrifugation, marker/probe complexes may be separated from uncomplexedassay components through a series of centrifugal steps, due to thedifferent sedimentation equilibria of complexes based on their differentsizes and densities (see, for example, Rivas and Minton (1993) TrendsBiochem. Sci. 18:284). Standard chromatographic techniques may also beutilized to separate complexed molecules from uncomplexed ones. Forexample, gel filtration chromatography separates molecules based onsize, and through the utilization of an appropriate gel filtration resinin a column format, for example, the relatively larger complex may beseparated from the relatively smaller uncomplexed components. Similarly,the relatively different charge properties of the marker/probe complexas compared to the uncomplexed components may be exploited todifferentiate the complex from uncomplexed components, for examplethrough the utilization of ion-exchange chromatography resins. Suchresins and chromatographic techniques are well known to one skilled inthe art (see, e.g., Heegaard (1998) J. MoI. Recognit. 11:141; Hage andTweed (1997) J. Chromatogr. B. Biomed. Sci. Appl. 12:499). Gelelectrophoresis may also be employed to separate complexed assaycomponents from unbound components (see, e.g., Ausubel et al, ed.,Current Protocols in Molecular Biology, John Wiley & Sons, New York,1987 1999). In this technique, protein or nucleic acid complexes areseparated based on size or charge, for example. In order to maintain thebinding interaction during the electrophoretic process, non-denaturinggel matrix materials and conditions in the absence of reducing agent aretypically preferred. Appropriate conditions to the particular assay andcomponents thereof will be well known to one skilled in the art.

In certain exemplary embodiments, the level of mRNA corresponding to themarker can be determined either by in situ and/or by in vitro formats ina biological sample using methods known in the art. Many expressiondetection methods use isolated RNA. For in vitro methods, any RNAisolation technique that does not select against the isolation of mRNAcan be utilized for the purification of RNA from blood cells (see, e.g.,Ausubel et al, ed., Current Protocols in Molecular Biology, John Wiley &Sons, New York 1987 1999). Additionally, large numbers of cells and/orsamples can readily be processed using techniques well known to those ofskill in the art, such as, for example, the single-step RNA isolationprocess of Chomczynski (1989, U.S. Pat. No. 4,843,155).

Isolated mRNA can be used in hybridization or amplification assays thatinclude, but are not limited to, Southern or Northern analyses,polymerase chain reaction analyses and probe arrays. In certainexemplary embodiments, a diagnostic method for the detection of mRNAlevels involves contacting the isolated mRNA with a nucleic acidmolecule (probe) that can hybridize to the mRNA encoded by the genebeing detected. The nucleic acid probe can be, for example, afull-length cDNA, or a portion thereof, such as an oligonucleotide of atleast 7, 15, 30, 50, 100, 250 or 500 nucleotides in length andsufficient to specifically hybridize under stringent conditions to anmRNA or genomic DNA encoding a marker of the present invention. Othersuitable probes for use in the diagnostic assays of the invention aredescribed herein. Hybridization of an mRNA with the probe indicates thatthe marker in question is being expressed.

In one format, the mRNA is immobilized on a solid surface and contactedwith a probe, for example by running the isolated mRNA on an agarose geland transferring the mRNA from the gel to a membrane, such asnitrocellulose. In an alternative format, the probe(s) are immobilizedon a solid surface and the mRNA is contacted with the probe(s), forexample, in a gene chip array. A skilled artisan can readily adapt knownmRNA detection methods for use in detecting the level of mRNA encoded bythe markers of the present invention.

An alternative method for determining the level of mRNA corresponding toa marker of the present invention in a sample involves the process ofnucleic acid amplification, e.g., by RT-PCR (the experimental embodimentset forth in U.S. Pat. Nos. 4,683,195 and 4,683,202), COLD-PCR (Li etal. (2008) Nat. Med. 14:579), ligase chain reaction (Barany, 1991, Proc.Natl. Acad. Sci. USA, 88:189), self sustained sequence replication(Guatelli et al., 1990, Proc. Natl. Acad. Sci. USA 87:1874),transcriptional amplification system (Kwoh et al. (1989) Proc. Natl.Acad. Sci. USA 86:1173), Q-Beta Replicase (Lizardi et al. (1988)Bio/Technology 6:1197), rolling circle replication (U.S. Pat. No.5,854,033) or any other nucleic acid amplification method, followed bythe detection of the amplified molecules using techniques well known tothose of skill in the art. These detection schemes are especially usefulfor the detection of nucleic acid molecules if such molecules arepresent in very low numbers. As used herein, amplification primers aredefined as being a pair of nucleic acid molecules that can anneal to 5′or 3′ regions of a gene (plus and minus strands, respectively, orvice-versa) and contain a short region in between. In general,amplification primers are from about 10 to 30 nucleotides in length andflank a region from about 50 to 200 nucleotides in length. Underappropriate conditions and with appropriate reagents, such primerspermit the amplification of a nucleic acid molecule comprising thenucleotide sequence flanked by the primers.

For in situ methods, mRNA does not need to be isolated from the sample(e.g., a bodily fluid (e.g., blood cells)) prior to detection. In suchmethods, a cell or tissue sample is prepared/processed using knownhistological methods. The sample is then immobilized on a support,typically a glass slide, and then contacted with a probe that canhybridize to mRNA that encodes the marker.

As an alternative to making determinations based on the absoluteexpression level of the marker, determinations may be based on thenormalized expression level of the marker. Expression levels arenormalized by correcting the absolute expression level of a marker bycomparing its expression to the expression of a gene that is not amarker, e.g., a housekeeping gene that is constitutively expressed.Suitable genes for normalization include housekeeping genes such as theactin gene, or epithelial cell-specific genes. This normalization allowsthe comparison of the expression level in a patient sample from onesource to a patient sample from another source, e.g., to compare apopulation of phagocytic from an individual to a population ofnon-phagocytic cells from the individual.

In one embodiment of this invention, a protein or polypeptidecorresponding to a marker is detected. In certain embodiments, an agentfor detecting a protein or polypeptide can be an antibody capable ofbinding to the polypeptide, such as an antibody with a detectable label.As used herein, the term “labeled,” with regard to a probe or antibody,is intended to encompass direct labeling of the probe or antibody bycoupling (i.e., physically linking) a detectable substance to the probeor antibody, as well as indirect labeling of the probe or antibody byreactivity with another reagent that is directly labeled. Examples ofindirect labeling include detection of a primary antibody using afluorescently labeled secondary antibody and end-labeling of a DNA probewith biotin such that it can be detected with fluorescently labeledstreptavidin. Antibodies can be polyclonal or monoclonal. An intactantibody, or a fragment thereof (e.g., Fab or F(ab′)2) can be used. Inone format, antibodies, or antibody fragments, can be used in methodssuch as Western blots or immunofluorescence techniques to detect theexpressed proteins. In such uses, it is generally preferable toimmobilize either the antibody or proteins on a solid support. Suitablesolid phase supports or carriers include any support capable of bindingan antigen or an antibody. Well known supports or carriers includeglass, polystyrene, polypropylene, polyethylene, dextran, nylon,amylases, natural and modified celluloses, polyacrylamides, gabbros,magnetite and the like.

A variety of formats can be employed to determine whether a samplecontains a protein that binds to a given antibody. Examples of suchformats include, but are not limited to, competitive and non-competitiveimmunoassay, enzyme immunoassay (EIA), radioimmunoassay (RIA), antigencapture assays, two-antibody sandwich assays, Western blot analysis,enzyme linked immunoabsorbant assay (ELISA), a planar array, acolorimetric assay, a chemiluminescent assay, a fluorescent assay, andthe like. Immunoassays, including radioimmmunoassays and enzyme-linkedimmunoassays, are useful in the methods of the present invention. Askilled artisan can readily adapt known protein/antibody detectionmethods for use in determining whether cells (e.g., bodily fluid cellssuch as blood cells) express a marker of the present invention.

One skilled in the art will know many other suitable carriers forbinding antibody or antigen, and will be able to adapt such support foruse with the present invention. For example, protein isolated from cells(e.g., bodily fluid cells such as blood cells) can be run on apolyacrylamide gel electrophoresis and immobilized onto a solid phasesupport such as nitrocellulose. The support can then be washed withsuitable buffers followed by treatment with the detectably labeledantibody. The solid phase support can then be washed with the buffer asecond time to remove unbound antibody. The amount of bound label on thesolid support can then be detected by conventional means.

In certain exemplary embodiments, assays are provided for diagnosis,prognosis, assessing the risk of developing prostate cancer, assessingthe efficacy of a treatment, monitoring the progression or regression ofprostate cancer, and identifying a compound capable of ameliorating ortreating prostate cancer. An exemplary method for these methods involvesobtaining a bodily fluid sample from a test subject, isolatingphagocytes and non-phagocytes, and contacting the phagocytes andnon-phagocytes with a compound or an agent capable of detecting one ormore of the markers of the disease or condition, e.g., marker nucleicacid (e.g., mRNA, genomic DNA), marker peptide (e.g., polypeptide orprotein), marker lipid (e.g., cholesterol), or marker metabolite (e.g.,creatinine) such that the presence of the marker is detected. In oneembodiment, an agent for detecting marker mRNA or genomic DNA is alabeled nucleic acid probe capable of hybridizing to marker mRNA orgenomic DNA. The nucleic acid probe can be, for example, a full-lengthmarker nucleic acid or a portion thereof. Other suitable probes for usein the diagnostic assays of the invention are described herein.

As used herein, a compound capable of ameliorating or treating prostatecancer can include, without limitations, any substance that can improvesymptoms or prognosis, prevent progression of the prostate cancer,promote regression of the prostate cancer, or eliminate the prostatecancer.

The methods of the invention can also be used to detect geneticalterations in a marker gene, thereby determining if a subject with thealtered gene is at risk for developing prostate cancer characterized bymisregulation in a marker protein activity or nucleic acid expression.In certain embodiments, the methods include detecting, in phagocytes,the presence or absence of a genetic alteration characterized by analteration affecting the integrity of a gene encoding a marker peptideand/or a marker gene. For example, such genetic alterations can bedetected by ascertaining the existence of at least one of: 1) a deletionof one or more nucleotides from one or more marker genes; 2) an additionof one or more nucleotides to one or more marker genes; 3) asubstitution of one or more nucleotides of one or more marker genes, 4)a chromosomal rearrangement of one or more marker genes; 5) analteration in the level of a messenger RNA transcript of one or moremarker genes; 6) aberrant modification of one or more marker genes, suchas of the methylation pattern of the genomic DNA; 7) the presence of anon-wild type splicing pattern of a messenger RNA transcript of one ormore marker genes; 8) a non-wild type level of a one or more markerproteins; 9) allelic loss of one or more marker genes; and 10)inappropriate post-translational modification of one or more markerproteins. As described herein, there are a large number of assays knownin the art which can be used for detecting alterations in one or moremarker genes.

In certain embodiments, detection of the alteration involves the use ofa probe/primer in a polymerase chain reaction (PCR) (see, e.g., U.S.Pat. Nos. 4,683,195, 4,683,202 and 5,854,033), such as real-time PCR,COLD-PCR (Li et al. (2008) Nat. Med. 14:579), anchor PCR, recursive PCRor RACE PCR, or, alternatively, in a ligation chain reaction (LCR) (see,e.g., Landegran et al. (1988) Science 241:1077; Prodromou and Pearl(1992) Protein Eng. 5:827; and Nakazawa et al. (1994) Proc. Natl. Acad.Sci. USA 91:360), the latter of which can be particularly useful fordetecting point mutations in a marker gene (see Abravaya et al. (1995)Nucleic Acids Res. 23:675). This method can include the steps ofcollecting a sample of cell free bodily fluid from a subject, isolatingnucleic acid (e.g., genomic, mRNA or both) from the sample, contactingthe nucleic acid sample with one or more primers which specificallyhybridize to a marker gene under conditions such that hybridization andamplification of the marker gene (if present) occurs, and detecting thepresence or absence of an amplification product, or detecting the sizeof the amplification product and comparing the length to a controlsample. It is anticipated that PCR and/or LCR may be desirable to use asa preliminary amplification step in conjunction with any of thetechniques used for detecting mutations described herein.

Alternative amplification methods include: self sustained sequencereplication (Guatelli et al., (1990) Proc. Natl. Acad. Sci. USA87:1874), transcriptional amplification system (Kwoh et al., (1989)Proc. Natl. Acad. Sci. USA 86:1173), Q Beta Replicase (Lizardi et al.(1988) Bio-Technology 6:1197), or any other nucleic acid amplificationmethod, followed by the detection of the amplified molecules usingtechniques well known to those of skill in the art. These detectionschemes are especially useful for the detection of nucleic acidmolecules if such molecules are present in very low numbers.

In an alternative embodiment, mutations in one or more marker genes froma sample can be identified by alterations in restriction enzyme cleavagepatterns. For example, sample and control DNA is isolated, optionallyamplified, digested with one or more restriction endonucleases, andfragment length sizes are determined by gel electrophoresis andcompared. Differences in fragment length sizes between sample andcontrol DNA indicates mutations in the sample DNA. Moreover, the use ofsequence specific ribozymes (see, for example, U.S. Pat. No. 5,498,531)can be used to score for the presence of specific mutations bydevelopment or loss of a ribozyme cleavage site.

In other embodiments, genetic mutations in one or more of the markersdescribed herein can be identified by hybridizing a sample and controlnucleic acids, e.g., DNA or RNA, to high density arrays containinghundreds or thousands of oligonucleotides probes (Cronin et al. (1996)Human Mutation 7: 244; Kozal et al. (1996) Nature Medicine 2:753). Forexample, genetic mutations in a marker nucleic acid can be identified intwo dimensional arrays containing light-generated DNA probes asdescribed in Cronin, M. T. et al. supra. Briefly, a first hybridizationarray of probes can be used to scan through long stretches of DNA in asample and control to identify base changes between the sequences bymaking linear arrays of sequential overlapping probes. This step allowsthe identification of point mutations. This step is followed by a secondhybridization array that allows the characterization of specificmutations by using smaller, specialized probe arrays complementary toall variants or mutations detected. Each mutation array is composed ofparallel probe sets, one complementary to the wild-type gene and theother complementary to the mutant gene.

In yet another embodiment, any of a variety of sequencing reactionsknown in the art can be used to directly sequence a marker gene anddetect mutations by comparing the sequence of the sample marker genewith the corresponding wild-type (control) sequence. Examples ofsequencing reactions include those based on techniques developed byMaxam and Gilbert ((1977) Proc. Natl. Acad. Sci. USA 74:560) or Sanger((1977) Proc. Natl. Acad. Sci. USA 74:5463). It is also contemplatedthat any of a variety of automated sequencing procedures can be utilizedwhen performing the diagnostic assays ((1995) Biotechniques 19:448),including sequencing by mass spectrometry (see, e.g., PCT InternationalPublication No. WO 94/16101; Cohen et al. (1996) Adv. Chromatogr.36:127-162; and Griffin et al. (1993) Appl. Biochem. Biotechnol.38:147).

Other methods for detecting mutations in a marker gene include methodsin which protection from cleavage agents is used to detect mismatchedbases in RNA/RNA or RNA/DNA heteroduplexes (Myers et al. (1985) Science230:1242). In general, the art technique of “mismatch cleavage” startsby providing heteroduplexes formed by hybridizing (labeled) RNA or DNAcontaining the wild-type marker sequence with potentially mutant RNA orDNA obtained from a tissue sample. The double-stranded duplexes aretreated with an agent which cleaves single-stranded regions of theduplex such as which will exist due to base pair mismatches between thecontrol and sample strands. For instance, RNA/DNA duplexes can betreated with RNase and DNA/DNA hybrids treated with 51 nuclease toenzymatically digesting the mismatched regions. In other embodiments,either DNA/DNA or RNA/DNA duplexes can be treated with hydroxylamine orosmium tetroxide and with piperidine in order to digest mismatchedregions. After digestion of the mismatched regions, the resultingmaterial is then separated by size on denaturing polyacrylamide gels todetermine the site of mutation. See, for example, Cotton et al. (1988)Proc. Natl. Acad. Sci. USA 85:4397; Saleeba et al. (1992) MethodsEnzymol. 217:286. In one embodiment, the control DNA or RNA can belabeled for detection.

In still another embodiment, the mismatch cleavage reaction employs oneor more proteins that recognize mismatched base pairs in double-strandedDNA (so called “DNA mismatch repair” enzymes) in defined systems fordetecting and mapping point mutations in marker cDNAs obtained fromsamples of cells. For example, the mutY enzyme of E. coli cleaves A atG/A mismatches and the thymidine DNA glycosylase from HeLa cells cleavesT at G/T mismatches (Hsu et al. (1994) Carcinogenesis 15:1657).According to an exemplary embodiment, a probe based on a markersequence, e.g., a wild-type marker sequence, is hybridized to a cDNA orother DNA product from a test cell(s). The duplex is treated with a DNAmismatch repair enzyme, and the cleavage products, if any, can bedetected from electrophoresis protocols or the like. See, for example,U.S. Pat. No. 5,459,039.

In other embodiments, alterations in electrophoretic mobility will beused to identify mutations in marker genes. For example, single strandconformation polymorphism (SSCP) may be used to detect differences inelectrophoretic mobility between mutant and wild type nucleic acids(Orita et al. (1989) Proc. Natl. Acad. Sci. USA 86:2766, see also Cotton(1993) Mutat. Res. 285:125; and Hayashi (1992) Genet. Anal. Tech. Appl.9:73). Single-stranded DNA fragments of sample and control markernucleic acids will be denatured and allowed to renature. The secondarystructure of single-stranded nucleic acids varies according to sequence,the resulting alteration in electrophoretic mobility enables thedetection of even a single base change. The DNA fragments may be labeledor detected with labeled probes. The sensitivity of the assay may beenhanced by using RNA (rather than DNA), in which the secondarystructure is more sensitive to a change in sequence. In one embodiment,the subject method utilizes heteroduplex analysis to separate doublestranded heteroduplex molecules on the basis of changes inelectrophoretic mobility (Keen et al. (1991) Trends Genet. 7:5).

In yet another embodiment the movement of mutant or wild-type fragmentsin polyacrylamide gels containing a gradient of denaturant is assayedusing denaturing gradient gel electrophoresis (DGGE) (Myers et al.(1985) Nature 313:495). When DGGE is used as the method of analysis, DNAwill be modified to insure that it does not completely denature, forexample by adding a GC clamp of approximately 40 bp of high-meltingGC-rich DNA by PCR. In a further embodiment, a temperature gradient isused in place of a denaturing gradient to identify differences in themobility of control and sample DNA (Rosenbaum and Reissner (1987)Biophys. Chem. 265:12753).

Examples of other techniques for detecting point mutations include, butare not limited to, selective oligonucleotide hybridization, selectiveamplification or selective primer extension. For example,oligonucleotide primers may be prepared in which the known mutation isplaced centrally and then hybridized to target DNA under conditionswhich permit hybridization only if a perfect match is found (Saiki etal. (1986) Nature 324:163; Saiki et al. (1989) Proc. Natl. Acad. Sci.USA 86:6230). Such allele specific oligonucleotides are hybridized toPCR amplified target DNA or a number of different mutations when theoligonucleotides are attached to the hybridizing membrane and hybridizedwith labeled target DNA.

Alternatively, allele specific amplification technology which depends onselective PCR amplification may be used in conjunction with the instantinvention. Oligonucleotides used as primers for specific amplificationmay carry the mutation of interest in the center of the molecule (sothat amplification depends on differential hybridization) (Gibbs et al.(1989) Nucl. Acids Res. 17:2437) or at the extreme 3′ end of one primerwhere, under appropriate conditions, mismatch can prevent, or reducepolymerase extension (Prossner (1993) Tibtech 11:238). In addition itmay be desirable to introduce a novel restriction site in the region ofthe mutation to create cleavage-based detection (Gasparini et al. (1992)Mol. Cell Probes 6:1). It is anticipated that in certain embodimentsamplification may also be performed using Taq ligase for amplification(Barany (1991) Proc. Natl. Acad. Sci. USA 88:189). In such cases,ligation will occur only if there is a perfect match at the 3′ end ofthe 5′ sequence making it possible to detect the presence of a knownmutation at a specific site by looking for the presence or absence ofamplification.

An exemplary method for detecting the presence or absence of an analyte(e.g., DNA, RNA, protein, polypeptide, or the like) corresponding to amarker of the invention in a biological sample involves obtaining abodily fluid sample (e.g., blood) from a test subject and contacting thebodily fluid sample with a compound or an agent capable of detecting oneor more markers. Detection methods described herein can be used todetect one or more markers in a biological sample in vitro as well as invivo. For example, in vitro techniques for detection of mRNA includeNorthern hybridizations and in situ hybridizations. In vitro techniquesfor detection of a polypeptide corresponding to a marker of theinvention include enzyme linked immunosorbent assays (ELISAs), Westernblots, immunoprecipitations and immunofluorescence. In vitro techniquesfor detection of genomic DNA include Southern hybridizations.Furthermore, in vivo techniques for detection of a polypeptidecorresponding to a marker of the invention include introducing into asubject a labeled antibody directed against the polypeptide. Forexample, the antibody can be labeled with a radioactive marker whosepresence and location in a subject can be detected by standard imagingtechniques. Because each marker is also an analyte, any method describedherein to detect the presence or absence of a marker can also be used todetect the presence or absence of an analyte.

The markers useful in the methods of the invention can include anymutation in any one of the markers. Mutation sites and sequences can beidentified, for example, by databases or repositories of suchinformation, e.g., The Human Gene Mutation Database (www.hgmd.cf.ac.uk),the Single Nucleotide Polymorphism Database (dbSNP,www.ncbi.nlm.nih.gov/projects/SNP), and the Online Mendelian Inheritancein Man (OMIM) website (www.ncbi.nlm.nih.gov/omim).

The present invention also provides kits that comprise marker detectionagents that detect at least one or more of the prostate cancer markersdescribed herein.

The present invention also provides methods of treating or preventingprostate cancer in a subject comprising administering to said subject anagent that modulates the activity or expression or disrupts the functionof at least one or more of the markers of this invention.

The one or more markers identified by this invention (e.g., markers inTables 1 and 2 and 3 and 4) may be used in the treatment of prostatecancer. For example, a marker (e.g., a protein or gene) identified bythe present invention may be used as a molecular target for atherapeutic agent. A marker identified by the invention also may be usedin any of the other methods of the invention, e.g., for monitoring theprogression or regression of a disease or condition. In certainembodiments, the one or more markers identified by the methods of thisinvention may have therapeutic potential. For example, if a marker isidentified as being up-regulated (or down-regulated), see, for example,the up-regulated (or down-regulated) markers in Tables 1 and 2 and 3 and4, or activated (or inhibited) in phagocytic cells from a subject havingprostate cancer, a compound or an agent that is capable ofdown-regulating (or up-regulating) or inhibiting (or activating) saidmarker may be useful in treating prostate cancer. Similarly, a geneprotein expression level, a protein expression level, or a combinationthereof may be useful in this aspect of the invention.

Unless otherwise defined herein, scientific and technical terms used inthis application shall have the meanings that are commonly understood bythose of ordinary skill in the art. Generally, nomenclature used inconnection with, and techniques of, cell and tissue culture, molecularbiology, cell and cancer biology, neurobiology, neurochemistry,virology, immunology, microbiology, pharmacology, genetics and proteinand nucleic acid chemistry, described herein, are those well known andcommonly used in the art.

All of the above, and any other publications, patents and publishedpatent applications referred to in this application are specificallyincorporated by reference herein. In case of conflict, the presentspecification, including its specific definitions, will control.

Throughout this specification, the word “comprise” or variations such as“comprises” or “comprising” will be understood to imply the inclusion ofa stated integer (or components) or group of integers (or components),but not the exclusion of any other integer (or components) or group ofintegers (or components).

The singular forms “a,” “an,” and “the” include the plurals unless thecontext clearly dictates otherwise.

The term “including” is used to mean “including but not limited to.”“Including” and “including but not limited to” are used interchangeably.

It is to be understood that the embodiments of the present inventionwhich have been described are merely illustrative of some of theapplications of the principles of the present invention. Numerousmodifications may be made by those skilled in the art based upon theteachings presented herein without departing from the true spirit andscope of the invention.

The following examples are set forth as being representative of thepresent invention. These examples are not to be construed as limitingthe scope of the invention as these and other equivalent embodimentswill be apparent in view of the present disclosure and accompanyingclaims.

Examples Example 1: Identification of Signature 1

A microarray was used to search for a signature of normal vs. aggressivecancer in subtraction-normalized expression data collected from bloodsamples processed 4 hours after collection (FIG. 1). Based on thisassay, the 117 genes of Signature 1 were selected and cross validated asdescribed in Example 5, below. Signature 1 had a sensitivity(probability of correctly detecting aggressive cancer) of 61%, and aspecificity (probability of correctly identifying normal patients) of58%.

TABLE 1 Signature 1 Upregulated (UR) or Signature Illumina AggressiveNormal downregulated (DR) in 1 marker # Transcript ID Gene name cancermean mean aggressive cancer 1 15689 OAS3 −9.0142958 −8.6439767 Cancer DR2 14409 RPL13L −1.2329318 −1.0853327 Cancer DR 3 20119 RDH5 29.318445829.7644395 Cancer DR 4 18791 SOX6 −1.9161712 −1.7990754 Cancer DR 510951 OSBPL1A −35.893494 −48.758773 Cancer UR 6 28512 GP5 10.97580383.5258523 Cancer UR 7 10695 GPR89A 10.5690901 10.9658205 Cancer DR 886688 HS.336511 −3.1086968 −2.8816541 Cancer DR 9 10875 TMEM80−47.885292 −46.725592 Cancer DR 10 13640 PPPDE2 −160.41714 −159.55055Cancer DR 11 22832 RYR3 −1.3796285 −1.265545 Cancer DR 12 168345 RHBDD277.0791083 79.0695935 Cancer DR 13 25536 MC1R 74.1685045 74.8626128Cancer DR 14 15079 CCDC128 7.1783549 −54.138047 Cancer UR 15 33909LOC285588 3.2824067 −1.8452802 Cancer UR 16 7272 ERGIC1 −76.02445−74.709689 Cancer DR 17 177008 H2BFWT −1.1260872 −0.9863237 Cancer DR 1820474 CYB561 124.258067 125.519911 Cancer DR 19 41366 LOC643879−0.1453645 0.0472667 Cancer DR 20 18811 RPL37 5.53447215 5.72682674Cancer DR 21 180795 UGT3A2 4.67348819 −1.6783285 Cancer UR 22 2007TP53I3 −141.98502 −140.64734 Cancer DR 23 16880 VWA5A −19.190299−18.947648 Cancer DR 24 123241 HS.571060 −1.460709 −1.3092629 Cancer DR25 4653 CREB1 1888.87492 1929.09126 Cancer DR 26 18195 CYP4F2 −2.3318799−2.2203552 Cancer DR 27 16552 TNFRSF11A −1.1759614 −1.0106681 Cancer DR28 5994 OAS2 −24.115038 −23.431537 Cancer DR 29 75591 HS.119922−0.9591632 −0.8249897 Cancer DR 30 166060 FLJ39632 −0.3382191 −0.1727163Cancer DR 31 8229 RP11-49G10.8 −6.0144268 −5.8367272 Cancer DR 32 18712KATNAL1 4.70953157 −1.8584848 Cancer UR 33 30114 GCNT2 −0.15947170.0188688 Cancer DR 34 346904 LOC729212 −0.476 −0.3228795 Cancer DR 35163101 IRF9 −392.03757 −380.96229 Cancer DR 36 33349 LOC653216−1.0175463 −0.8626032 Cancer DR 37 42341 LOC440386 −0.8536411 −0.6714295Cancer DR 38 6769 INF2 3.25469335 3.48877586 Cancer DR 39 15843 JARID2−380.58538 −378.03988 Cancer DR 40 17229 HNRNPM 32.3962097 36.4189036Cancer DR 41 1894 IL5RA 0.83011712 1.23681659 Cancer DR 42 182198 YOD1−1.0684564 −0.968089 Cancer DR 43 21388 VHL −153.61908 −149.34478 CancerDR 44 11812 TRIM56 96.3762478 97.9483118 Cancer DR 45 347804LOC100130276 29.0218497 29.6648654 Cancer DR 46 27308 UBE2I −1.5908237−1.459543 Cancer DR 47 11362 C8ORF30A −2.8852459 −2.7452391 Cancer DR 4815490 METT11D1 119.293311 120.326483 Cancer DR 49 29227 ZSCAN22 0.5475680.68218938 Cancer DR 50 16766 ZNF385B −0.7907855 −0.6223701 Cancer DR 5124801 C20ORF94 0.40482839 0.81268385 Cancer DR 52 173747 D4S234E531.294243 538.45889 Cancer DR 53 23467 C7ORF20 −33.821791 −33.360883Cancer DR 54 170201 CCDC88C 200.919891 203.185051 Cancer DR 55 2163KRT38 4.69638401 −1.994684 Cancer UR 56 162122 LOC727735 3.0613806−2.517745 Cancer UR 57 171831 LOC732215 −0.9351387 −0.8075807 Cancer DR58 343768 LOC646353 −0.8575194 −0.7297925 Cancer DR 59 21343 DPRX2.98927307 −2.5628675 Cancer UR 60 23908 SLC2A14 −4.387825 −4.1721651Cancer DR 61 341890 LOC732446 −0.6644245 −0.5321704 Cancer DR 62 33455RNF5P1 −82.512422 −80.617845 Cancer DR 63 22073 MEST −0.6877526−0.5880494 Cancer DR 64 338462 LOC100130829 2.19340981 −3.3179853 CancerUR 65 31584 LOC646223 −4.695691 −4.5120316 Cancer DR 66 13066 C19ORF50−130.26601 −128.0409 Cancer DR 67 11344 VPS16 −74.322484 −71.72812Cancer DR 68 28868 TCEAL1 −2.2433124 −2.1065912 Cancer DR 69 6866 TRIM2843.6841007 44.7414677 Cancer DR 70 138370 ANKRD13D −54.17119 −52.791341Cancer DR 71 180926 STX6 −190.67106 −189.13492 Cancer DR 72 28557 AGFG245.1171985 45.500398 Cancer DR 73 179882 IL17RD 251.863927 258.077015Cancer DR 74 162687 BCR 8.03158781 8.21889719 Cancer DR 75 176690 SP100−15.413932 −14.913489 Cancer DR 76 12053 RASL10B 3.75650279 −2.8100791Cancer UR 77 71322 HS.13291 −22.921159 −22.296491 Cancer DR 78 17081C1ORF188 16.3121173 16.6240139 Cancer DR 79 13590 NMNAT2 2.45548587−2.5067911 Cancer UR 80 7282 CTHRC1 0.73487218 0.89298341 Cancer DR 8118789 ASS1 −1.6801724 −1.5631152 Cancer DR 82 352616 LOC791120163.351813 164.477126 Cancer DR 83 34136 LOC649493 −0.6295056 −0.4795787Cancer DR 84 346345 FLJ31306 21.087961 21.6361882 Cancer DR 85 29344VGLL4 49.4631916 50.6916039 Cancer DR 86 336512 LOC100132568 −1.6082874−1.4598448 Cancer DR 87 6870 TCEB3C −1.8559032 −1.7141848 Cancer DR 8812233 SBDSP 29.0236367 29.6106915 Cancer DR 89 338504 LOC100132535−0.0770285 0.17556409 Cancer DR 90 11118 C8ORF37 609.519491 637.907911Cancer DR 91 14405 GOLGA8B 2542.72843 2556.47364 Cancer DR 92 593 SOLH−5.8111916 −5.2700925 Cancer DR 93 15604 LOC400464 50.0233917 50.473654Cancer DR 94 22944 NKX6-1 2.1845754 −2.4379099 Cancer UR 95 163801LOC442517 −0.1049745 0.0275036 Cancer DR 96 29810 ATP1B4 2.37077671−2.1346992 Cancer UR 97 167794 USP41 −2.2619871 −2.0813413 Cancer DR 98388123 MIR30E −0.2759666 −0.1673701 Cancer DR 99 138008 HAND2 −0.7726292−0.6345135 Cancer DR 100 177432 CASP7 −10.080261 −9.8616229 Cancer DR101 1696 ZNF347 3.20338016 3.42245148 Cancer DR 102 40864 LOC65359829.5211839 29.9100599 Cancer DR 103 33044 LOC401238 −6.4844928−6.2037945 Cancer DR 104 39554 LOC440014 −0.4051124 −0.2520049 Cancer DR105 175279 LOC339352 14.5986659 14.8643875 Cancer DR 106 23490 NEK7−5.929757 −5.8008051 Cancer DR 107 181743 LOC646463 −4.1358791−3.8487266 Cancer DR 108 15634 CCL8 −73.189981 −71.419617 Cancer DR 10934049 LOC642196 3.6810006 −2.3531877 Cancer UR 110 79403 HS.15734410.0794538 10.4426597 Cancer DR 111 7196 DHX9 −4.7593833 −3.934944Cancer DR 112 44285 LOC388237 1.03869502 1.19389418 Cancer DR 113 178108KCNJ14 0.41681205 0.56043169 Cancer DR 114 166167 OR7G3 −0.6721556−0.5410997 Cancer DR 115 18273 GLTSCR1 33.8096356 34.5040224 Cancer DR116 1736 NOMO2 −112.57512 −109.84641 Cancer DR 117 175566 WDR3742.7679257 46.0837328 Cancer DR

Example 2: Identification of Signature 2

A microarray was used to search for a signature of normal vs. aggressivecancer in subtraction-normalized expression data collected from bloodsamples processed 4 hours after collection. The assay was used to searchfor stable transcripts (defined as those in the top 1,000 differentiallyexpressed genes, with subtraction normalization at 4 hours) that had anexpression level ratio of 0.8 to 1.25 in samples processed 48 hoursafter collection compared to 4 hours after collection (FIG. 2). Based onthis assay, 18 genes were selected and cross validated as described inExample 5, below. Signature 2 had a sensitivity (probability ofcorrectly detecting aggressive cancer) of 60%, and a specificity(probability of correctly identifying normal patients) of 66%.

TABLE 2 Signature 2 Upregulated (UR) or Signature Illumina AggressiveNormal downregulated (DR) in 2 marker # Transcript ID Gene name cancermean mean aggressive cancer 1 175412 REPS2 0.14613724 −7.5068116 CancerUR 2 33909 LOC285588 3.2824067 −1.8452802 Cancer UR 3 22438 C20ORF1122.62604692 −4.0643154 Cancer UR 4 337363 DIPAS 1.06084697 −3.2177178Cancer UR 5 165657 TPRX1 1.79654397 −2.8351934 Cancer UR 6 38966FLJ16369 1.13600879 −2.5978003 Cancer UR 7 44021 LOC652255 3.03708564−1.7358787 Cancer UR 8 41116 LOC642130 2.03361554 −1.9989049 Cancer UR 921343 DPRX 2.98927307 −2.5628675 Cancer UR 10 339666 LOC4402251.72985119 −2.6607478 Cancer UR 11 91353 HS.434989 1.08668984 −2.5889165Cancer UR 12 40621 LOC642335 2.69733599 −2.2656365 Cancer UR 13 369972GGTLC1 1.04843521 −3.889128 Cancer UR 14 32275 LOC642966 4.72677994−2.0890642 Cancer UR 15 22944 NKX6-1 2.1845754 −2.4379099 Cancer UR 1617458 GPC5 0.40241623 −4.2203747 Cancer UR 17 13240 RASGEF1C 0.83201981−3.3957263 Cancer UR 18 22752 ACOT11 2.83207957 −2.2946388 Cancer UR

Example 3: Identification of Signature 3

A microarray was used as in Example 2 to search for a signature ofnormal vs. aggressive cancer in subtraction-normalized expression datacollected from blood samples processed 4 hours after collection. Basedon this assay, 18 genes were selected and cross validated as describedin Example 5, below. Signature 3 had a sensitivity (probability ofcorrectly detecting aggressive cancer) of 45%, and a specificity(probability of correctly identifying normal patients) of 64%.

TABLE 3 Signature 3 Upregulated (UR) or Signature Illumina AggressiveNormal downregulated (DR) in 3 marker # Transcript ID Gene name cancermean mean aggressive cancer 1 175412 REPS2 0.14613724 −7.5068116 CancerUR 2 33909 LOC285588 3.2824067 −1.8452802 Cancer UR 3 22438 C20ORF1122.62604692 −4.0643154 Cancer UR 4 337363 DIPAS 1.06084697 −3.2177178Cancer UR 5 165657 TPRX1 1.79654397 −2.8351934 Cancer UR 6 38966FLJ16369 1.13600879 −2.5978003 Cancer UR 7 44021 LOC652255 3.03708564−1.7358787 Cancer UR 8 41116 LOC642130 2.03361554 −1.9989049 Cancer UR 921343 DPRX 2.98927307 −2.5628675 Cancer UR 10 339666 LOC4402251.72985119 −2.6607478 Cancer UR 11 91353 HS.434989 1.08668984 −2.5889165Cancer UR 12 40621 LOC642335 2.69733599 −2.2656365 Cancer UR 13 369972GGTLC1 1.04843521 −3.889128 Cancer UR 14 32275 LOC642966 4.72677994−2.0890642 Cancer UR 15 22944 NKX6-1 2.1845754 −2.4379099 Cancer UR 1617458 GPC5 0.40241623 −4.2203747 Cancer UR 17 13240 RASGEF1C 0.83201981−3.3957263 Cancer UR 18 22752 ACOT11 2.83207957 −2.2946388 Cancer UR

Example 4: Identification of Signature 4

A microarray was used to search for a signature of normal vs. aggressivecancer in subtraction-normalized expression data collected from bloodsamples processed 4 hours after collection. Based on this assay, the 10genes of Signature 4 were selected and cross validated as described inExample 5, below. Signature 4 had a sensitivity (probability ofcorrectly detecting aggressive cancer) of 64%, and a specificity(probability of correctly identifying normal patients) of 58%.

TABLE 4 Signature 4 Upregulated (UR) or Signature Illumina AggressiveNormal downregulated (DR) in 4 marker # Transcript ID Gene name cancermean mean aggressive cancer 1 8276 C3ORF26 7.1783549 −54.138047 CancerUR 2 22171 FOXA3 3.2824067 −1.8452802 Cancer UR 3 1150 FANCB 4.67348819−1.6783285 Cancer UR 4 162004 ALDH9A1 4.70953157 −1.8584848 Cancer UR 5334559 LOC100133080 4.69638401 −1.994684 Cancer UR 6 19987 NR2E13.75650279 −2.8100791 Cancer UR 7 90347 HS.413397 2.45548587 −2.5067911Cancer UR 8 7726 NSUN7 2.1845754 −2.4379099 Cancer UR 9 34808 LOC6510442.37077671 −2.1346992 Cancer UR 10 364878 PCBP2 3.6810006 −2.3531877Cancer UR

Example 5: Statistical Analysis of Microarray Data

Working with microarray data can be challenging because large numbers ofgenes can increase the likelihood of false positives, while a smallnumber of samples can lead to overfitting. These issues can be overcomeby using statistical methods to reduce the false rate of positives andusing independent training and test data sets (e.g., cross-validation)to avoid overfitting. In particular, instead of using a “typical” 5%significance level, the false discovery rate (FDR) can be controlled toensure that only 5% of the genes that are discovered are falsepositives, and Empirical Bayesian estimates can be used to improve teststatistics.

Because an overfit model will perform poorly on an independent test set,a good test of the fit of a model is how well is performs on anindependent test set. For small sample sizes, splitting data into testand training sets may leave too small of a data set for good training.This issue can be solved by using cross-validation, which splits thedata into K-folds, trains the method on K−1 of the folds, and tests themethod on the last fold. The ideal split for cross-validation is 10-foldfor accurate and precise estimates of diagnostic accuracy. In a 10-foldcross validation, however, there are more than 10 splits because thereare many choices for which data points go into the folds. For example,with the microarray data collected as described above, there are50,979,600 ways to form 90% training/10% testing data sets.

The Empirical Bayesian method was used as follows:

-   -   1. The differential gene expression (DE) of macrophages vs. T        cells was calculated for each gene. DE is expressed as the log        of the ratio of phagocyte to T cell expression:        DE=log(GE_(P)/GE_(TC)), where GE_(P) is phagocyte gene        expression and GE_(TC) is T cell gene expression.    -   2. The mean DE was compared in cancer and control patients with        a two-sample t-test. Empirical Bayes estimates of the test        statistics “shrink” these toward zero.    -   3. Calculate a diagnostic signature with K genes:

$S = {\sum\limits_{i = 1}^{K}{w_{i}( {{DE}_{i} - \mu_{i}} )}}$

-   -   If S>0, then the patient was diagnosed with cancer.    -   4. The number of genes K to include in the signature was        determined by comparing misclassification rates in independent        test sets with cross-validation.        Errors were calculated using an average of 1-sensitivity and        1-specificity, and the cross-validated error was used to select        markers.

Using the above methods, the markers associated with aggressive prostatecancer in macrophages vs. T cells (Tables 1 and 2) were identified.

What is claimed is:
 1. A method for diagnosing or aiding in thediagnosis of prostate cancer in a subject, the method comprising thesteps of: a) measuring the levels of one or more markers selected fromthe group consisting of Signature 1 markers in a population of thesubject's macrophage cells; b) measuring the levels of the one or moreselected Signature 1 markers in a population of the subject'snon-phagocytic cells; and c) identifying a difference between themeasured levels of the one or more selected Signature 1 markers in stepsa) and b), wherein the identified difference indicates that the subjecthas said prostate cancer.
 2. A method for assessing the risk ofdeveloping prostate cancer in a subject, the method comprising the stepsof: a) measuring the levels of one or more markers selected from thegroup consisting of Signature 1 markers in a population of the subject'smacrophage cells; b) measuring the levels of the one or more selectedSignature 1 markers in a population of the subject's non-phagocyticcells; and c) identifying a difference between the measured levels ofthe one or more selected Signature 1 markers in steps a) and b), whereinthe identified difference indicates that the subject has a risk ofdeveloping said prostate cancer.
 3. A method for prognosing or aiding inthe prognosis of prostate cancer in a subject, the method comprising thesteps of: a) measuring the levels of one or more markers selected fromthe group consisting of Signature 1 markers in a population of thesubject's macrophage cells; b) measuring the levels of the one or moreselected Signature 1 markers in a population of the subject'snon-phagocytic cells; and c) identifying a difference between themeasured levels of the one or more selected Signature 1 markers in stepsa) and b), wherein the identified difference is indicative of theprognosis of said prostate cancer in the subject.
 4. A method forassessing the efficacy of a treatment for prostate cancer in a subjectcomprising: a) measuring the levels of one or more markers selected fromthe group consisting of Signature 1 markers in a population of thesubject's macrophage cells before the treatment; b) measuring the levelsof the one or more selected Signature 1 markers in a population of thesubject's non-phagocytic cells before the treatment; c) identifying afirst difference between the measured levels of the one or more selectedSignature 1 markers in steps a) and b); d) measuring the levels of theone or more selected Signature 1 markers in a population of thesubject's macrophage cells after the treatment; e) measuring the levelsof the one or more selected Signature 1 markers in a population of thesubject's non-phagocytic cells after the treatment; f) identifying asecond difference between the measured levels of the one or moreselected Signature 1 markers in steps d) and e); and g) identifying adifference between the first difference and the second difference,wherein the difference identified in g) is indicative of the efficacy ofthe treatment for said prostate cancer in the subject.
 5. A method formonitoring the progression or regression of prostate cancer in a subjectcomprising: a) measuring the levels of one or more markers selected fromthe group consisting of Signature 1 markers in a population of thesubject's macrophage cells at a first time point; b) measuring thelevels of the one or more selected Signature 1 markers in a populationof the subject's non-phagocytic cells at the first time point; c)identifying a first difference between the measured levels of the one ormore selected Signature 1 markers in steps a) and b); d) measuring thelevels of the one or more selected Signature 1 markers in a populationof the subject's macrophage cells at a second time point; e) measuringthe levels of the one or more selected Signature 1 markers in apopulation of the subject's non-phagocytic cells at the second timepoint; f) identifying a second difference between the measured levels ofthe one or more selected Signature 1 markers in steps d) and e); and g)identifying a difference between the first difference and the seconddifference, wherein the difference identified in g) is indicative of theprogression or regression of said prostate cancer in the subject.
 6. Amethod for identifying a compound capable of ameliorating or treatingprostate cancer in a subject comprising: a) measuring the levels of oneor more markers selected from the group consisting of Signature 1markers in a population of the subject's macrophage cells beforeadministering the compound to the subject; b) measuring the levels ofthe one or more selected Signature 1 markers in a population of thesubject's non-phagocytic cells before administering the compound to thesubject; c) identifying a first difference between the measured levelsof the one or more selected Signature 1 markers in steps a) and b); d)measuring the levels of the one or more selected Signature 1 markers ina population of the subject's macrophage cells after the administrationof the compound; e) measuring the levels of the one or more selectedSignature 1 markers in a population of the subject's non-phagocyticcells after the administration of the compound; f) identifying a seconddifference between the measured levels of the one or more selectedSignature 1 markers in steps d) and e); and g) identifying a differencebetween the first difference and the second difference, wherein thedifference identified in g) indicates that the compound is capable ofameliorating or treating said prostate cancer in the subject.
 7. Amethod for diagnosing or aiding in the diagnosis of prostate cancer in asubject, the method comprising the steps of: a) measuring the levels ofone or more markers selected from the group consisting of Signature 2markers in a population of the subject's macrophage cells; b) measuringthe levels of the one or more selected Signature 2 markers in apopulation of the subject's non-phagocytic cells; and c) identifying adifference between the measured levels of the one or more selectedSignature 2 markers in steps a) and b), wherein the identifieddifference indicates that the subject has said prostate cancer.
 8. Amethod for assessing the risk of developing prostate cancer in asubject, the method comprising the steps of: a) measuring the levels ofone or more markers selected from the group consisting of Signature 2markers in a population of the subject's macrophage cells; b) measuringthe levels of the one or more selected Signature 2 markers in apopulation of the subject's non-phagocytic cells; and c) identifying adifference between the measured levels of the one or more selectedSignature 2 markers in steps a) and b), wherein the identifieddifference indicates that the subject has a risk of developing saidprostate cancer.
 9. A method for prognosing or aiding in the prognosisof prostate cancer in a subject, the method comprising the steps of: a)measuring the levels of one or more markers selected from the groupconsisting of Signature 2 markers in a population of the subject'smacrophage cells; b) measuring the levels of the one or more selectedSignature 2 markers in a population of the subject's non-phagocyticcells; and c) identifying a difference between the measured levels ofthe one or more selected Signature 2 markers in steps a) and b), whereinthe identified difference is indicative of the prognosis of saidprostate cancer in the subject.
 10. A method for assessing the efficacyof a treatment for prostate cancer in a subject comprising: a) measuringthe levels of one or more markers selected from the group consisting ofSignature 2 markers in a population of the subject's macrophage cellsbefore the treatment; b) measuring the levels of the one or moreselected Signature 2 markers in a population of the subject'snon-phagocytic cells before the treatment; c) identifying a firstdifference between the measured levels of the one or more selectedSignature 2 markers in steps a) and b); d) measuring the levels of theone or more selected Signature 2 markers in a population of thesubject's macrophage cells after the treatment; e) measuring the levelsof the one or more selected Signature 2 markers in a population of thesubject's non-phagocytic cells after the treatment; f) identifying asecond difference between the measured levels of the one or moreselected Signature 2 markers in steps d) and e); and g) identifying adifference between the first difference and the second difference,wherein the difference identified in g) is indicative of the efficacy ofthe treatment for said prostate cancer in the subject.
 11. A method formonitoring the progression or regression of prostate cancer in a subjectcomprising: a) measuring the levels of one or more markers selected fromthe group consisting of Signature 2 markers in a population of thesubject's macrophage cells at a first time point; b) measuring thelevels of the one or more selected Signature 2 markers in a populationof the subject's non-phagocytic cells at the first time point; c)identifying a first difference between the measured levels of the one ormore selected Signature 2 markers in steps a) and b); d) measuring thelevels of the one or more selected Signature 2 markers in a populationof the subject's macrophage cells at a second time point; e) measuringthe levels of the one or more selected Signature 2 markers in apopulation of the subject's non-phagocytic cells at the second timepoint; f) identifying a second difference between the measured levels ofthe one or more selected Signature 2 markers in steps d) and e); and g)identifying a difference between the first difference and the seconddifference, wherein the difference identified in g) is indicative of theprogression or regression of said prostate cancer in the subject.
 12. Amethod for identifying a compound capable of ameliorating or treatingprostate cancer in a subject comprising: a) measuring the levels of oneor more markers selected from the group consisting of Signature 2markers in a population of the subject's macrophage cells beforeadministering the compound to the subject; b) measuring the levels ofthe one or more selected Signature 2 markers in a population of thesubject's non-phagocytic cells before administering the compound to thesubject; c) identifying a first difference between the measured levelsof the one or more selected Signature 2 markers in steps a) and b); d)measuring the levels of the one or more selected Signature 2 markers ina population of the subject's macrophage cells after the administrationof the compound; e) measuring the levels of the one or more selectedSignature 2 markers in a population of the subject's non-phagocyticcells after the administration of the compound; f) identifying a seconddifference between the measured levels of the one or more selectedSignature 2 markers in steps d) and e); and g) identifying a differencebetween the first difference and the second difference, wherein thedifference identified in g) indicates that the compound is capable ofameliorating or treating said prostate cancer in the subject.
 13. Amethod for diagnosing or aiding in the diagnosis of prostate cancer in asubject, the method comprising the steps of: a) measuring the levels ofone or more markers selected from the group consisting of Signature 3markers in a population of the subject's macrophage cells; b) measuringthe levels of the one or more selected Signature 3 markers in apopulation of the subject's non-phagocytic cells; and c) identifying adifference between the measured levels of the one or more selectedSignature 3 markers in steps a) and b), wherein the identifieddifference indicates that the subject has said prostate cancer.
 14. Amethod for assessing the risk of developing prostate cancer in asubject, the method comprising the steps of: a) measuring the levels ofone or more markers selected from the group consisting of Signature 3markers in a population of the subject's macrophage cells; b) measuringthe levels of the one or more selected Signature 3 markers in apopulation of the subject's non-phagocytic cells; and c) identifying adifference between the measured levels of the one or more selectedSignature 3 markers in steps a) and b), wherein the identifieddifference indicates that the subject has a risk of developing saidprostate cancer.
 15. A method for prognosing or aiding in the prognosisof prostate cancer in a subject, the method comprising the steps of: a)measuring the levels of one or more markers selected from the groupconsisting of Signature 3 markers in a population of the subject'smacrophage cells; b) measuring the levels of the one or more selectedSignature 3 markers in a population of the subject's non-phagocyticcells; and c) identifying a difference between the measured levels ofthe one or more selected Signature 3 markers in steps a) and b), whereinthe identified difference is indicative of the prognosis of saidprostate cancer in the subject.
 16. A method for assessing the efficacyof a treatment for prostate cancer in a subject comprising: a) measuringthe levels of one or more markers selected from the group consisting ofSignature 3 markers in a population of the subject's macrophage cellsbefore the treatment; b) measuring the levels of the one or moreselected Signature 3 markers in a population of the subject'snon-phagocytic cells before the treatment; c) identifying a firstdifference between the measured levels of the one or more selectedSignature 3 markers in steps a) and b); d) measuring the levels of theone or more selected Signature 3 markers in a population of thesubject's macrophage cells after the treatment; e) measuring the levelsof the one or more selected Signature 3 markers in a population of thesubject's non-phagocytic cells after the treatment; f) identifying asecond difference between the measured levels of the one or moreselected Signature 3 markers in steps d) and e); and g) identifying adifference between the first difference and the second difference,wherein the difference identified in g) is indicative of the efficacy ofthe treatment for said prostate cancer in the subject.
 17. A method formonitoring the progression or regression of prostate cancer in a subjectcomprising: a) measuring the levels of one or more markers selected fromthe group consisting of Signature 3 markers in a population of thesubject's macrophage cells at a first time point; b) measuring thelevels of the one or more selected Signature 3 markers in a populationof the subject's non-phagocytic cells at the first time point; c)identifying a first difference between the measured levels of the one ormore selected Signature 3 markers in steps a) and b); d) measuring thelevels of the one or more selected Signature 3 markers in a populationof the subject's macrophage cells at a second time point; e) measuringthe levels of the one or more selected Signature 3 markers in apopulation of the subject's non-phagocytic cells at the second timepoint; f) identifying a second difference between the measured levels ofthe one or more selected Signature 3 markers in steps d) and e); and g)identifying a difference between the first difference and the seconddifference, wherein the difference identified in g) is indicative of theprogression or regression of said prostate cancer in the subject.
 18. Amethod for identifying a compound capable of ameliorating or treatingprostate cancer in a subject comprising: a) measuring the levels of oneor more markers selected from the group consisting of Signature 3markers in a population of the subject's macrophage cells beforeadministering the compound to the subject; b) measuring the levels ofthe one or more selected Signature 3 markers in a population of thesubject's non-phagocytic cells before administering the compound to thesubject; c) identifying a first difference between the measured levelsof the one or more selected Signature 3 markers in steps a) and b); d)measuring the levels of the one or more selected Signature 3 markers ina population of the subject's macrophage cells after the administrationof the compound; e) measuring the levels of the one or more selectedSignature 3 markers in a population of the subject's non-phagocyticcells after the administration of the compound; f) identifying a seconddifference between the measured levels of the one or more selectedSignature 3 markers in steps d) and e); and g) identifying a differencebetween the first difference and the second difference, wherein thedifference identified in g) indicates that the compound is capable ofameliorating or treating said prostate cancer in the subject.
 19. Amethod for diagnosing or aiding in the diagnosis of prostate cancer in asubject, the method comprising the steps of: a) measuring the levels ofone or more markers selected from the group consisting of Signature 4markers in a population of the subject's macrophage cells; b) measuringthe levels of the one or more selected Signature 4 markers in apopulation of the subject's non-phagocytic cells; and c) identifying adifference between the measured levels of the one or more selectedSignature 4 markers in steps a) and b), wherein the identifieddifference indicates that the subject has said prostate cancer.
 20. Amethod for assessing the risk of developing prostate cancer in asubject, the method comprising the steps of: a) measuring the levels ofone or more markers selected from the group consisting of Signature 4markers in a population of the subject's macrophage cells; b) measuringthe levels of the one or more selected Signature 4 markers in apopulation of the subject's non-phagocytic cells; and c) identifying adifference between the measured levels of the one or more selectedSignature 4 markers in steps a) and b), wherein the identifieddifference indicates that the subject has a risk of developing saidprostate cancer.
 21. A method for prognosing or aiding in the prognosisof prostate cancer in a subject, the method comprising the steps of: a)measuring the levels of one or more markers selected from the groupconsisting of Signature 4 markers in a population of the subject'smacrophage cells; b) measuring the levels of the one or more selectedSignature 4 markers in a population of the subject's non-phagocyticcells; and c) identifying a difference between the measured levels ofthe one or more selected Signature 4 markers in steps a) and b), whereinthe identified difference is indicative of the prognosis of saidprostate cancer in the subject.
 22. A method for assessing the efficacyof a treatment for prostate cancer in a subject comprising: a) measuringthe levels of one or more markers selected from the group consisting ofSignature 4 markers in a population of the subject's macrophage cellsbefore the treatment; b) measuring the levels of the one or moreselected Signature 4 markers in a population of the subject'snon-phagocytic cells before the treatment; c) identifying a firstdifference between the measured levels of the one or more selectedSignature 4 markers in steps a) and b); d) measuring the levels of theone or more selected Signature 4 markers in a population of thesubject's macrophage cells after the treatment; e) measuring the levelsof the one or more selected Signature 4 markers in a population of thesubject's non-phagocytic cells after the treatment; f) identifying asecond difference between the measured levels of the one or moreselected Signature 4 markers in steps d) and e); and g) identifying adifference between the first difference and the second difference,wherein the difference identified in g) is indicative of the efficacy ofthe treatment for said prostate cancer in the subject.
 23. A method formonitoring the progression or regression of prostate cancer in a subjectcomprising: a) measuring the levels of one or more markers selected fromthe group consisting of Signature 4 markers in a population of thesubject's macrophage cells at a first time point; b) measuring thelevels of the one or more selected Signature 4 markers in a populationof the subject's non-phagocytic cells at the first time point; c)identifying a first difference between the measured levels of the one ormore selected Signature 4 markers in steps a) and b); d) measuring thelevels of the one or more selected Signature 4 markers in a populationof the subject's macrophage cells at a second time point; e) measuringthe levels of the one or more selected Signature 4 markers in apopulation of the subject's non-phagocytic cells at the second timepoint; f) identifying a second difference between the measured levels ofthe one or more selected Signature 4 markers in steps d) and e); and g)identifying a difference between the first difference and the seconddifference, wherein the difference identified in g) is indicative of theprogression or regression of said prostate cancer in the subject.
 24. Amethod for identifying a compound capable of ameliorating or treatingprostate cancer in a subject comprising: a) measuring the levels of oneor more markers selected from the group consisting of Signature 4markers in a population of the subject's macrophage cells beforeadministering the compound to the subject; b) measuring the levels ofthe one or more selected Signature 4 markers in a population of thesubject's non-phagocytic cells before administering the compound to thesubject; c) identifying a first difference between the measured levelsof the one or more selected Signature 4 markers in steps a) and b); d)measuring the levels of the one or more selected Signature 4 markers ina population of the subject's macrophage cells after the administrationof the compound; e) measuring the levels of the one or more selectedSignature 4 markers in a population of the subject's non-phagocyticcells after the administration of the compound; f) identifying a seconddifference between the measured levels of the one or more selectedSignature 4 markers in steps d) and e); and g) identifying a differencebetween the first difference and the second difference, wherein thedifference identified in g) indicates that the compound is capable ofameliorating or treating said prostate cancer in the subject.
 25. Amethod for diagnosing or aiding in the diagnosis of prostate cancer in asubject, the method comprising the steps of: a) measuring the levels ofone or more markers selected from the group consisting of Signature 1markers in a population of the subject's neutrophil cells; b) measuringthe levels of the one or more selected Signature 1 markers in apopulation of the subject's non-phagocytic cells; and c) identifying adifference between the measured levels of the one or more selectedSignature 1 markers in steps a) and b), wherein the identifieddifference indicates that the subject has said prostate cancer.
 26. Amethod for assessing the risk of developing prostate cancer in asubject, the method comprising the steps of: a) measuring the levels ofone or more markers selected from the group consisting of Signature 1markers in a population of the subject's neutrophil cells; b) measuringthe levels of the one or more selected Signature 1 markers in apopulation of the subject's non-phagocytic cells; and c) identifying adifference between the measured levels of the one or more selectedSignature 1 markers in steps a) and b), wherein the identifieddifference indicates that the subject has a risk of developing saidprostate cancer.
 27. A method for prognosing or aiding in the prognosisof prostate cancer in a subject, the method comprising the steps of: a)measuring the levels of one or more markers selected from the groupconsisting of Signature 1 markers in a population of the subject'sneutrophil cells; b) measuring the levels of the one or more selectedSignature 1 markers in a population of the subject's non-phagocyticcells; and c) identifying a difference between the measured levels ofthe one or more selected Signature 1 markers in steps a) and b), whereinthe identified difference is indicative of the prognosis of saidprostate cancer in the subject.
 28. A method for assessing the efficacyof a treatment for prostate cancer in a subject comprising: a) measuringthe levels of one or more markers selected from the group consisting ofSignature 1 markers in a population of the subject's neutrophil cellsbefore the treatment; b) measuring the levels of the one or moreselected Signature 1 markers in a population of the subject'snon-phagocytic cells before the treatment; c) identifying a firstdifference between the measured levels of the one or more selectedSignature 1 markers in steps a) and b); d) measuring the levels of theone or more selected Signature 1 markers in a population of thesubject's neutrophil cells after the treatment; e) measuring the levelsof the one or more selected Signature 1 markers in a population of thesubject's non-phagocytic cells after the treatment; f) identifying asecond difference between the measured levels of the one or moreselected Signature 1 markers in steps d) and e); and g) identifying adifference between the first difference and the second difference,wherein the difference identified in g) is indicative of the efficacy ofthe treatment for said prostate cancer in the subject.
 29. A method formonitoring the progression or regression of prostate cancer in a subjectcomprising: a) measuring the levels of one or more markers selected fromthe group consisting of Signature 1 markers in a population of thesubject's neutrophil cells at a first time point; b) measuring thelevels of the one or more selected Signature 1 markers in a populationof the subject's non-phagocytic cells at the first time point; c)identifying a first difference between the measured levels of the one ormore selected Signature 1 markers in steps a) and b); d) measuring thelevels of the one or more selected Signature 1 markers in a populationof the subject's neutrophil cells at a second time point; e) measuringthe levels of the one or more selected Signature 1 markers in apopulation of the subject's non-phagocytic cells at the second timepoint; f) identifying a second difference between the measured levels ofthe one or more selected Signature 1 markers in steps d) and e); and g)identifying a difference between the first difference and the seconddifference, wherein the difference identified in g) is indicative of theprogression or regression of said prostate cancer in the subject.
 30. Amethod for identifying a compound capable of ameliorating or treatingprostate cancer in a subject comprising: a) measuring the levels of oneor more markers selected from the group consisting of Signature 1markers in a population of the subject's neutrophil cells beforeadministering the compound to the subject; b) measuring the levels ofthe one or more selected Signature 1 markers in a population of thesubject's non-phagocytic cells before administering the compound to thesubject; c) identifying a first difference between the measured levelsof the one or more selected Signature 1 markers in steps a) and b); d)measuring the levels of the one or more selected Signature 1 markers ina population of the subject's neutrophil cells after the administrationof the compound; e) measuring the levels of the one or more selectedSignature 1 markers in a population of the subject's non-phagocyticcells after the administration of the compound; f) identifying a seconddifference between the measured levels of the one or more selectedSignature 1 markers in steps d) and e); and g) identifying a differencebetween the first difference and the second difference, wherein thedifference identified in g) indicates that the compound is capable ofameliorating or treating said prostate cancer in the subject.
 31. Amethod for diagnosing or aiding in the diagnosis of prostate cancer in asubject, the method comprising the steps of: a) measuring the levels ofone or more markers selected from the group consisting of Signature 2markers in a population of the subject's neutrophil cells; b) measuringthe levels of the one or more selected Signature 2 markers in apopulation of the subject's non-phagocytic cells; and c) identifying adifference between the measured levels of the one or more selectedSignature 2 markers in steps a) and b), wherein the identifieddifference indicates that the subject has said prostate cancer.
 32. Amethod for assessing the risk of developing prostate cancer in asubject, the method comprising the steps of: a) measuring the levels ofone or more markers selected from the group consisting of Signature 2markers in a population of the subject's neutrophil cells; b) measuringthe levels of the one or more selected Signature 2 markers in apopulation of the subject's non-phagocytic cells; and c) identifying adifference between the measured levels of the one or more selectedSignature 2 markers in steps a) and b), wherein the identifieddifference indicates that the subject has a risk of developing saidprostate cancer.
 33. A method for prognosing or aiding in the prognosisof prostate cancer in a subject, the method comprising the steps of: a)measuring the levels of one or more markers selected from the groupconsisting of Signature 2 markers in a population of the subject'sneutrophil cells; b) measuring the levels of the one or more selectedSignature 2 markers in a population of the subject's non-phagocyticcells; and c) identifying a difference between the measured levels ofthe one or more selected Signature 2 markers in steps a) and b), whereinthe identified difference is indicative of the prognosis of saidprostate cancer in the subject.
 34. A method for assessing the efficacyof a treatment for prostate cancer in a subject comprising: a) measuringthe levels of one or more markers selected from the group consisting ofSignature 2 markers in a population of the subject's neutrophil cellsbefore the treatment; b) measuring the levels of the one or moreselected Signature 2 markers in a population of the subject'snon-phagocytic cells before the treatment; c) identifying a firstdifference between the measured levels of the one or more selectedSignature 2 markers in steps a) and b); d) measuring the levels of theone or more selected Signature 2 markers in a population of thesubject's neutrophil cells after the treatment; e) measuring the levelsof the one or more selected Signature 2 markers in a population of thesubject's non-phagocytic cells after the treatment; f) identifying asecond difference between the measured levels of the one or moreselected Signature 2 markers in steps d) and e); and g) identifying adifference between the first difference and the second difference,wherein the difference identified in g) is indicative of the efficacy ofthe treatment for said prostate cancer in the subject.
 35. A method formonitoring the progression or regression of prostate cancer in a subjectcomprising: a) measuring the levels of one or more markers selected fromthe group consisting of Signature 2 markers in a population of thesubject's neutrophil cells at a first time point; b) measuring thelevels of the one or more selected Signature 2 markers in a populationof the subject's non-phagocytic cells at the first time point; c)identifying a first difference between the measured levels of the one ormore selected Signature 2 markers in steps a) and b); d) measuring thelevels of the one or more selected Signature 2 markers in a populationof the subject's neutrophil cells at a second time point; e) measuringthe levels of the one or more selected Signature 2 markers in apopulation of the subject's non-phagocytic cells at the second timepoint; f) identifying a second difference between the measured levels ofthe one or more selected Signature 2 markers in steps d) and e); and g)identifying a difference between the first difference and the seconddifference, wherein the difference identified in g) is indicative of theprogression or regression of said prostate cancer in the subject.
 36. Amethod for identifying a compound capable of ameliorating or treatingprostate cancer in a subject comprising: a) measuring the levels of oneor more markers selected from the group consisting of Signature 2markers in a population of the subject's neutrophil cells beforeadministering the compound to the subject; b) measuring the levels ofthe one or more selected Signature 2 markers in a population of thesubject's non-phagocytic cells before administering the compound to thesubject; c) identifying a first difference between the measured levelsof the one or more selected Signature 2 markers in steps a) and b); d)measuring the levels of the one or more selected Signature 2 markers ina population of the subject's neutrophil cells after the administrationof the compound; e) measuring the levels of the one or more selectedSignature 2 markers in a population of the subject's non-phagocyticcells after the administration of the compound; f) identifying a seconddifference between the measured levels of the one or more selectedSignature 2 markers in steps d) and e); and g) identifying a differencebetween the first difference and the second difference, wherein thedifference identified in g) indicates that the compound is capable ofameliorating or treating said prostate cancer in the subject.
 37. Amethod for diagnosing or aiding in the diagnosis of prostate cancer in asubject, the method comprising the steps of: a) measuring the levels ofone or more markers selected from the group consisting of Signature 3markers in a population of the subject's neutrophil cells; b) measuringthe levels of the one or more selected Signature 3 markers in apopulation of the subject's non-phagocytic cells; and c) identifying adifference between the measured levels of the one or more selectedSignature 3 markers in steps a) and b), wherein the identifieddifference indicates that the subject has said prostate cancer.
 38. Amethod for assessing the risk of developing prostate cancer in asubject, the method comprising the steps of: a) measuring the levels ofone or more markers selected from the group consisting of Signature 3markers in a population of the subject's neutrophil cells; b) measuringthe levels of the one or more selected Signature 3 markers in apopulation of the subject's non-phagocytic cells; and c) identifying adifference between the measured levels of the one or more selectedSignature 3 markers in steps a) and b), wherein the identifieddifference indicates that the subject has a risk of developing saidprostate cancer.
 39. A method for prognosing or aiding in the prognosisof prostate cancer in a subject, the method comprising the steps of: a)measuring the levels of one or more markers selected from the groupconsisting of Signature 3 markers in a population of the subject'sneutrophil cells; b) measuring the levels of the one or more selectedSignature 3 markers in a population of the subject's non-phagocyticcells; and c) identifying a difference between the measured levels ofthe one or more selected Signature 3 markers in steps a) and b), whereinthe identified difference is indicative of the prognosis of saidprostate cancer in the subject.
 40. A method for assessing the efficacyof a treatment for prostate cancer in a subject comprising: a) measuringthe levels of one or more markers selected from the group consisting ofSignature 3 markers in a population of the subject's neutrophil cellsbefore the treatment; b) measuring the levels of the one or moreselected Signature 3 markers in a population of the subject'snon-phagocytic cells before the treatment; c) identifying a firstdifference between the measured levels of the one or more selectedSignature 3 markers in steps a) and b); d) measuring the levels of theone or more selected Signature 3 markers in a population of thesubject's neutrophil cells after the treatment; e) measuring the levelsof the one or more selected Signature 3 markers in a population of thesubject's non-phagocytic cells after the treatment; f) identifying asecond difference between the measured levels of the one or moreselected Signature 3 markers in steps d) and e); and g) identifying adifference between the first difference and the second difference,wherein the difference identified in g) is indicative of the efficacy ofthe treatment for said prostate cancer in the subject.
 41. A method formonitoring the progression or regression of prostate cancer in a subjectcomprising: a) measuring the levels of one or more markers selected fromthe group consisting of Signature 3 markers in a population of thesubject's neutrophil cells at a first time point; b) measuring thelevels of the one or more selected Signature 3 markers in a populationof the subject's non-phagocytic cells at the first time point; c)identifying a first difference between the measured levels of the one ormore selected Signature 3 markers in steps a) and b); d) measuring thelevels of the one or more selected Signature 3 markers in a populationof the subject's neutrophil cells at a second time point; e) measuringthe levels of the one or more selected Signature 3 markers in apopulation of the subject's non-phagocytic cells at the second timepoint; f) identifying a second difference between the measured levels ofthe one or more selected Signature 3 markers in steps d) and e); and g)identifying a difference between the first difference and the seconddifference, wherein the difference identified in g) is indicative of theprogression or regression of said prostate cancer in the subject.
 42. Amethod for identifying a compound capable of ameliorating or treatingprostate cancer in a subject comprising: a) measuring the levels of oneor more markers selected from the group consisting of Signature 3markers in a population of the subject's neutrophil cells beforeadministering the compound to the subject; b) measuring the levels ofthe one or more selected Signature 3 markers in a population of thesubject's non-phagocytic cells before administering the compound to thesubject; c) identifying a first difference between the measured levelsof the one or more selected Signature 3 markers in steps a) and b); d)measuring the levels of the one or more selected Signature 3 markers ina population of the subject's neutrophil cells after the administrationof the compound; e) measuring the levels of the one or more selectedSignature 3 markers in a population of the subject's non-phagocyticcells after the administration of the compound; f) identifying a seconddifference between the measured levels of the one or more selectedSignature 3 markers in steps d) and e); and g) identifying a differencebetween the first difference and the second difference, wherein thedifference identified in g) indicates that the compound is capable ofameliorating or treating said prostate cancer in the subject.
 43. Amethod for diagnosing or aiding in the diagnosis of prostate cancer in asubject, the method comprising the steps of: a) measuring the levels ofone or more markers selected from the group consisting of Signature 4markers in a population of the subject's neutrophil cells; b) measuringthe levels of the one or more selected Signature 4 markers in apopulation of the subject's non-phagocytic cells; and c) identifying adifference between the measured levels of the one or more selectedSignature 4 markers in steps a) and b), wherein the identifieddifference indicates that the subject has said prostate cancer.
 44. Amethod for assessing the risk of developing prostate cancer in asubject, the method comprising the steps of: a) measuring the levels ofone or more markers selected from the group consisting of Signature 4markers in a population of the subject's neutrophil cells; b) measuringthe levels of the one or more selected Signature 4 markers in apopulation of the subject's non-phagocytic cells; and c) identifying adifference between the measured levels of the one or more selectedSignature 4 markers in steps a) and b), wherein the identifieddifference indicates that the subject has a risk of developing saidprostate cancer.
 45. A method for prognosing or aiding in the prognosisof prostate cancer in a subject, the method comprising the steps of: a)measuring the levels of one or more markers selected from the groupconsisting of Signature 4 markers in a population of the subject'sneutrophil cells; b) measuring the levels of the one or more selectedSignature 4 markers in a population of the subject's non-phagocyticcells; and c) identifying a difference between the measured levels ofthe one or more selected Signature 4 markers in steps a) and b), whereinthe identified difference is indicative of the prognosis of saidprostate cancer in the subject.
 46. A method for assessing the efficacyof a treatment for prostate cancer in a subject comprising: a) measuringthe levels of one or more markers selected from the group consisting ofSignature 4 markers in a population of the subject's neutrophil cellsbefore the treatment; b) measuring the levels of the one or moreselected Signature 4 markers in a population of the subject'snon-phagocytic cells before the treatment; c) identifying a firstdifference between the measured levels of the one or more selectedSignature 4 markers in steps a) and b); d) measuring the levels of theone or more selected Signature 4 markers in a population of thesubject's neutrophil cells after the treatment; e) measuring the levelsof the one or more selected Signature 4 markers in a population of thesubject's non-phagocytic cells after the treatment; f) identifying asecond difference between the measured levels of the one or moreselected Signature 4 markers in steps d) and e); and g) identifying adifference between the first difference and the second difference,wherein the difference identified in g) is indicative of the efficacy ofthe treatment for said prostate cancer in the subject.
 47. A method formonitoring the progression or regression of prostate cancer in a subjectcomprising: a) measuring the levels of one or more markers selected fromthe group consisting of Signature 4 markers in a population of thesubject's neutrophil cells at a first time point; b) measuring thelevels of the one or more selected Signature 4 markers in a populationof the subject's non-phagocytic cells at the first time point; c)identifying a first difference between the measured levels of the one ormore selected Signature 4 markers in steps a) and b); d) measuring thelevels of the one or more selected Signature 4 markers in a populationof the subject's neutrophil cells at a second time point; e) measuringthe levels of the one or more selected Signature 4 markers in apopulation of the subject's non-phagocytic cells at the second timepoint; f) identifying a second difference between the measured levels ofthe one or more selected Signature 4 markers in steps d) and e); and g)identifying a difference between the first difference and the seconddifference, wherein the difference identified in g) is indicative of theprogression or regression of said prostate cancer in the subject.
 48. Amethod for identifying a compound capable of ameliorating or treatingprostate cancer in a subject comprising: a) measuring the levels of oneor more markers selected from the group consisting of Signature 4markers in a population of the subject's neutrophil cells beforeadministering the compound to the subject; b) measuring the levels ofthe one or more selected Signature 4 markers in a population of thesubject's non-phagocytic cells before administering the compound to thesubject; c) identifying a first difference between the measured levelsof the one or more selected Signature 4 markers in steps a) and b); d)measuring the levels of the one or more selected Signature 4 markers ina population of the subject's neutrophil cells after the administrationof the compound; e) measuring the levels of the one or more selectedSignature 4 markers in a population of the subject's non-phagocyticcells after the administration of the compound; f) identifying a seconddifference between the measured levels of the one or more selectedSignature 4 markers in steps d) and e); and g) identifying a differencebetween the first difference and the second difference, wherein thedifference identified in g) indicates that the compound is capable ofameliorating or treating said prostate cancer in the subject.
 49. Themethod of any one of claims 1-48, further comprising measuring at leastone standard parameter associated with said prostate cancer.
 50. Themethod of claim 49, wherein the standard parameter is selected from thegroup consisting of tumor stage, tumor grade, tumor size, tumor visualcharacteristics, tumor growth, tumor thickness, tumor progression, tumormetastasis tumor distribution within the body, odor, molecularpathology, genomics, or tumor angiograms.
 51. The method of any one ofclaims 1-24, wherein the selected Signature 1, Signature 2, Signature 3,or Signature 4 markers are up-regulated or activated in the macrophagecells compared to the non-phagocytic cells.
 52. The method of any one ofclaims 1-24, wherein the selected Signature 1, Signature 2, Signature 3,or Signature 4 markers are down-regulated or inhibited in the macrophagecells compared to the non-phagocytic cells.
 53. The method of any one ofclaims 1-24, wherein the selected Signature 1, Signature 2, Signature 3,or Signature 4 markers are up-regulated or activated in the neutrophilcells compared to the non-phagocytic cells.
 54. The method of any one ofclaims 1-24, wherein the selected Signature 1, Signature 2, Signature 3,or Signature 4 markers are down-regulated or inhibited in the neutrophilcells compared to the non-phagocytic cells.
 55. The method of any one ofclaim 1-6 or 25-30, wherein at least two, three, four, five, six, seven,eight, nine, ten, or eleven markers are selected from Signature
 1. 56.The method of any one of claim 7-12 or 31-36, wherein at least two,three, four, five, six, seven, eight, nine, ten, or eleven markers areselected from Signature
 2. 57. The method of any one of claim 13-18 or37-42, wherein at least two, three, four, five, six, seven, eight, nine,ten, or eleven markers are selected from Signature
 3. 58. The method ofany one of claim 19-24 or 43-48, wherein at least two, three, four,five, six, seven, eight, nine, ten, or eleven markers are selected fromSignature
 4. 59. The method of any one of claims 1-24, furthercomprising lysing the macrophage cells and the non-phagocytic cellsbefore a).
 60. The method of any one of claims 1-24, further comprisingextracting the cellular contents from the macrophage cells and thenon-phagocytic cells before a).
 61. The method of any one of claims25-48, further comprising lysing the neutrophil cells and thenon-phagocytic cells before a).
 62. The method of any one of claims25-48, further comprising extracting the cellular contents from theneutrophil cells and the non-phagocytic cells before a).
 63. The methodof claim 60, wherein the cellular contents of the macrophage cellscomprise viable diseased cells, dead diseased cells, apoptotic diseasedcells, circulating tumor cells, infectious agents, fetal cells,trophoblasts, or fragments thereof.
 64. The method of claim 62, whereinthe cellular contents of the neutrophil cells comprise viable diseasedcells, dead diseased cells, apoptotic diseased cells, circulating tumorcells, infectious agents, fetal cells, trophoblasts, or fragmentsthereof.
 65. The method of claim 60, wherein the selected one or moremarkers are present in the cellular contents of the macrophage cells.66. The method of any one of claims 1-48, wherein the non-phagocyticcells are T cells, B cells, null cells, basophils, or mixtures thereof.67. The method of any one of claims 1-24, wherein the macrophage cellsare isolated from a bodily fluid sample, tissues, or cells of thesubject.
 68. The method of any one of claims 25-48, wherein theneutrophil cells are isolated from a bodily fluid sample, tissues, orcells of the subject.
 69. The method of any one of claims 1-48, whereinthe non-phagocytic cells are isolated from a bodily fluid sample,tissues, or cells of the subject.
 70. The method of any one of claims67-69, wherein the bodily fluid sample is blood, urine, stool, saliva,lymph fluid, cerebrospinal fluid, synovial fluid, cystic fluid, ascites,pleural effusion, fluid obtained from a pregnant woman in the firsttrimester, fluid obtained from a pregnant woman in the second trimester,fluid obtained from a pregnant woman in the third trimester, maternalblood, amniotic fluid, chorionic villus sample, fluid from apreimplantation embryo, maternal urine, maternal saliva, placentalsample, fetal blood, lavage and cervical vaginal fluid, interstitialfluid, or ocular fluid.
 71. The method of any one of claims 1-24,wherein the macrophage cells are isolated using antibodies, using aligand that binds to a molecular receptor expressed on the plasmamembranes of white blood cells, or by flow cytometry, fluorescenceactivated cell sorting, filtration, gradient-based centrifugation,elution, microfluidics, magnetic separation technique,fluorescent-magnetic separation technique, nanostructure, quantum dots,high throughput microscope-based platforms, or a combination thereof.72. The method of any one of claims 25-48, wherein the neutrophil cellsare isolated using antibodies, using a ligand that binds to a molecularreceptor expressed on the plasma membranes of white blood cells, or byflow cytometry, fluorescence activated cell sorting, filtration,gradient-based centrifugation, elution, microfluidics, magneticseparation technique, fluorescent-magnetic separation technique,nanostructure, quantum dots, high throughput microscope-based platforms,or a combination thereof.
 73. The method of any one of claims 1-48,wherein the non-phagocytic cells are isolated using antibodies, using aligand that binds to a molecular receptor expressed on the plasmamembranes of white blood cells, or by flow cytometry, fluorescenceactivated cell sorting, filtration, gradient-based centrifugation,elution, microfluidics, magnetic separation technique,fluorescent-magnetic separation technique, nanostructure, quantum dots,high throughput microscope-based platforms, or a combination thereof.74. The method of any one of claims 1-24, wherein the macrophage cellsare isolated using a product secreted by the macrophage cells.
 75. Themethod of any one of claims 25-48, wherein the neutrophil cells areisolated by using a product secreted by the neutrophil cells.
 76. Themethod of any one the claims 1-24, wherein the macrophage cells areisolated by using a cell surface target on the surface of macrophagecells.
 77. The method of any one of claims 25-48, wherein the neutrophilcells are isolated by using a cell surface target on the surface ofneutrophil cells.
 78. The method of claim 76, wherein the target isexpressed by the macrophage cells.
 79. The method of claim 76, whereinthe target is not expressed by the macrophage cells.
 80. The method ofclaim 77, wherein the target is expressed by the neutrophil cells. 81.The method of claim 77, wherein the target is not expressed by theneutrophil cells.
 82. The method of any one of claims 76-81, wherein thetarget is a marker of said prostate cancer.
 83. The method of any one ofclaims 1-48, wherein the measured levels are gene expression levels. 84.The method of any one of claims 1-48, wherein the measured levels areprotein expression levels.
 85. The method of any one of the claim 1-48,wherein the levels or activities are measured by a qualitative assay, aquantitative assay, or a combination thereof.
 86. The method of claim85, wherein the quantitative assay uses sequencing, direct sequencing,RNA sequencing, whole transcriptome shotgun sequencing, random shotgunsequencing, Sanger dideoxy termination sequencing, whole-genomesequencing, sequencing by hybridization, pyrosequencing, capillaryelectrophoresis, gel electrophoresis, duplex sequencing, cyclesequencing, single-base extension sequencing, solid-phase sequencing,high-throughput sequencing, massively parallel signature sequencing,emulsion PCR, sequencing by reversible dye terminator, paired-endsequencing, near-term sequencing, exonuclease sequencing, sequencing byligation, short-read sequencing, single-molecule sequencing,sequencing-by-synthesis, real-time sequencing, reverse-terminatorsequencing, nanopore sequencing, 454 sequencing, Solexa Genome Analyzersequencing, SOLiD® sequencing, MS-PET sequencing, mass spectrometry,matrix assisted laser desorption/ionization-time of flight (MALDI-TOF)mass spectrometry, electrospray ionization (ESI) mass spectrometry,surface-enhanced laser desorption/ionization-time of flight (SELDI-TOF)mass spectrometry, quadrupole-time of flight (Q-TOF) mass spectrometry,atmospheric pressure photoionization mass spectrometry (APPI-MS),Fourier transform mass spectrometry (FTMS), matrix-assisted laserdesorption/ionization-Fourier transform-ion cyclotron resonance(MALDI-FT-ICR) mass spectrometry, secondary ion mass spectrometry(SIMS), polymerase chain reaction (PCR) analysis, quantitative PCR,real-time PCR, fluorescence assay, colorimetric assay, chemiluminescentassay, or a combination thereof.
 87. The method of claim 83, wherein thegene expression levels are measured by polymerase chain reaction (PCR)analysis, sequencing analysis, electrophoretic analysis, restrictionfragment length polymorphism (RFLP) analysis, Northern blot analysis,quantitative PCR, reverse-transcriptase-PCR analysis (RT-PCR),allele-specific oligonucleotide hybridization analysis, comparativegenomic hybridization, heteroduplex mobility assay (HMA), single strandconformational polymorphism (SSCP), denaturing gradient gelelectrophisis (DGGE), RNAase mismatch analysis, mass spectrometry,tandem mass spectrometry, matrix assisted laserdesorption/ionization-time of flight (MALDI-TOF) mass spectrometry,electrospray ionization (ESI) mass spectrometry, surface-enhanced laserdesorption/ionization-time of flight (SELDI-TOF) mass spectrometry,quadrupole-time of flight (Q-TOF) mass spectrometry, atmosphericpressure photoionization mass spectrometry (APPI-MS), Fourier transformmass spectrometry (FTMS), matrix-assisted laserdesorption/ionization-Fourier transform-ion cyclotron resonance(MALDI-FT-ICR) mass spectrometry, secondary ion mass spectrometry(SIMS), surface plasmon resonance, Southern blot analysis, in situhybridization, fluorescence in situ hybridization (FISH), chromogenic insitu hybridization (CISH), immunohistochemistry (IHC), microarray,comparative genomic hybridization, karyotyping, multiplexligation-dependent probe amplification (MLPA), Quantitative MultiplexPCR of Short Fluorescent Fragments (QMPSF), microscopy, methylationspecific PCR (MSP) assay, HpaII tiny fragment Enrichment byLigation-mediated PCR (HELP) assay, radioactive acetate labeling assays,colorimetric DNA acetylation assay, chromatin immunoprecipitationcombined with microarray (ChIP-on-chip) assay, restriction landmarkgenomic scanning, Methylated DNA immunoprecipitation (MeDIP), molecularbreak light assay for DNA adenine methyltransferase activity,chromatographic separation, methylation-sensitive restriction enzymeanalysis, bisulfite-driven conversion of non-methylated cytosine touracil, methyl-binding PCR analysis, or a combination thereof.
 88. Themethod of claim 83, wherein the gene expression levels are measured by asequencing technique selected from the group consisting of directsequencing, RNA sequencing, whole transcriptome shotgun sequencing,random shotgun sequencing, Sanger dideoxy termination sequencing,whole-genome sequencing, sequencing by hybridization, pyrosequencing,capillary electrophoresis, gel electrophoresis, duplex sequencing, cyclesequencing, single-base extension sequencing, solid-phase sequencing,high-throughput sequencing, massively parallel signature sequencing,emulsion PCR, sequencing by reversible dye terminator, paired-endsequencing, near-term sequencing, exonuclease sequencing, sequencing byligation, short-read sequencing, single-molecule sequencing,sequencing-by-synthesis, real-time sequencing, reverse-terminatorsequencing, nanopore sequencing, 454 sequencing, Solexa Genome Analyzersequencing, SOLiD® sequencing, MS-PET sequencing, mass spectrometry, anda combination thereof.
 89. The method of claim 84, wherein the proteinexpression levels are measured by an immunohistochemistry assay, anenzyme-linked immunosorbent assay (ELISA), in situ hybridization,chromatography, liquid chromatography, size exclusion chromatography,high performance liquid chromatography (HPLC), gas chromatography, massspectrometry, tandem mass spectrometry, matrix assisted laserdesorption/ionization-time of flight (MALDI-TOF) mass spectrometry,electrospray ionization (ESI) mass spectrometry, surface-enhanced laserdesorption/ionization-time of flight (SELDI-TOF) mass spectrometry,quadrupole-time of flight (Q-TOF) mass spectrometry, atmosphericpressure photoionization mass spectrometry (APPI-MS), Fourier transformmass spectrometry (FTMS), matrix-assisted laserdesorption/ionization-Fourier transform-ion cyclotron resonance(MALDI-FT-ICR) mass spectrometry, secondary ion mass spectrometry(SIMS), radioimmunoassays, microscopy, microfluidic chip-based assays,surface plasmon resonance, sequencing, Western blotting assay, or acombination thereof.
 90. The method of any one the claims 1-89, whereinthe subject is a mammal.
 91. The method of claim 90, wherein the subjectis a human.
 92. The method of any one the claims 1-48, wherein thedifference is greater than a 1-fold difference.
 93. The method of claim92, wherein the difference is at least 1.05-fold, 1.1-fold, 1.2-fold,1.3-fold, 1.4-fold, 1.5-fold, 2-fold, 2.5-fold, 3-fold, 4-fold, 5-fold,6-fold, 7-fold, 8-fold, 9-fold, or 10-fold difference.
 94. A kit formeasuring the levels of at least one or more markers selected from thegroup consisting of Signature 1 markers, comprising reagents forspecifically measuring the levels of the selected Signature 1 marker.95. A kit for measuring the levels of at least one or more markersselected from the group consisting of Signature 2 markers, comprisingreagents for specifically measuring the levels of the selected Signature2 marker.
 96. A kit for measuring the levels of at least one or moremarkers selected from the group consisting of Signature 3 markers,comprising reagents for specifically measuring the levels of theselected Signature 3 marker.
 97. A kit for measuring the levels of atleast one or more markers selected from the group consisting ofSignature 4 markers, comprising reagents for specifically measuring thelevels of the selected Signature 4 marker.
 98. The kit of any one ofclaims 95 and 96, wherein the reagents comprise one or more antibodiesor fragments thereof, oligonucleotides, or aptamers.
 99. A method oftreating or preventing prostate cancer in a subject comprisingadministering to said subject an agent that modulates the activity orexpression of at least one or more markers selected from the groupconsisting of Signature
 1. 100. A method of treating or preventingprostate cancer in a subject comprising administering to said subject anagent that modulates the activity or expression of at least one or moremarkers selected from the group consisting of Signature
 2. 101. A methodof treating or preventing prostate cancer in a subject comprisingadministering to said subject an agent that modulates the activity orexpression of at least one or more markers selected from the groupconsisting of Signature
 3. 102. A method of treating or preventingprostate cancer in a subject comprising administering to said subject anagent that modulates the activity or expression of at least one or moremarkers selected from the group consisting of Signature
 4. 103. Themethod of any one of claims 99-102, wherein the agent is a smallmolecule modulator, siRNA, or an antibody or fragment thereof.